Nutrient accumulation and transcriptome patterns during grain development in rice

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

Effects of silicate stabilizers on cadmium reduction and the quality of rice grains in acidic paddy soil

Silicate has been proven to be highly-effective at immobilizing soil heavy metals, but the effects of silicate stabilizers on rice grain cadmium (Cd) reduction and rice quality under field conditions are not clear. In this study, a field experiment was conducted over three consecutive years was conducted to examine the Cd reduction in rice grains and to reveal the potential effects of silicate stabilizers on rice grain nutrients, by setting different amounts of bentonite (B), silica‒calcium fertilizer (SC) and zeolite powder (ZP). The results revealed that the application of the B, SC and ZP significantly decreased the soil CaCl2‒Cd concentration (> 39%) and significantly reduced the grain Cd concentration in both early rice (> 70%) and late rice (> 18%) under field conditions; the silicate stabilizers reduced the soil available iron (Fe) but did not limit rice grain Fe nutrition. Additionally, the three silicates promoted rice yield and improved the rice grain Ca and Mg contents; and the application of B increased the amylose concentration of the late rice grains. In conclusion, high amounts of silicate stabilizers did not adversely influence the soil conventional nutrient indices, rice minerals or rice taste, but changes in rice selenium content need attention. Overall, in comparison with lime, silicate stabilizers can improve not only the safety of rice but also the nutritional and taste qualities of rice and are more eco-friendly for long-term use in soil.

Phenotypic and transcriptomic responses of diverse rice accessions to transient heat stress during early grain development

Heat stress (HS) occurring during the grain-filling period has a detrimental effect on grain yield and quality in rice (Oryza sativa). The development of heat-resilient cultivars could partly solve this issue if tolerant alleles can be identified and incorporated into the germplasm. In this study, we posit that some of the phenotypic variations for heat resilience during grain development could be due to variations in gene expression among accessions. To test this, we characterized the HS response of 10 diverse rice accessions from three major sub-populations using physiological and transcriptome analyses. At a single-grain level, grain width and grain thickness emerged as the most heat-sensitive traits. During a transient HS, IND-3 was categorized as highly sensitive, while five accessions exhibited moderate heat sensitivity, and four accessions were tolerant. Only a core set of 29.4% of the differentially expressed genes was common to the three rice sub-populations. Heat-tolerant accession TEJ-5 uniquely triggered an unfolded protein response (UPR) under HS, as evident from the induction of OsbZIP50 and downstream UPR genes. OsbZIP58, a gene that positively regulates grain filling, was more highly induced by HS in IND-2 despite its moderate heat sensitivity. Collectively, our analysis suggests that both unique gene expression responses and variation in the level of responses for a given pathway distinguish diverse accessions. Only some of these responses are associated with single-grain phenotypes in a manner consistent with the known roles of these genes and pathways.

Moisture content and mycorrhizal fungi in maternal environment influence performance and composition of Lallemantia species offspring

The availability of soil water content and nutrition in the maternal plant environment plays pivotal roles in shaping the performance, physio-biochemical properties, and chemical composition of the produced seed. This study aimed to investigate the effects of water and arbuscular mycorrhizal fungi (AMF) of maternal plant environment on performance, physio-biochemical properties, and chemical compositions of Lallemantia species offspring. A split-factorial experiment was performed using a randomized complete block design (RCBD) with three replications. The main plot consisted of three drought stress (30 %, 60 % and 90 % of soil available water depletion). The subplots were the factorial combination of arbuscular mycorrhizal fungi (AMF- and AMF+) and Lallemantia species (L. iberica and L. royleana). The offspring of both Lallemantia species experienced a decrease in seed performance, superoxide dismutase, catalase, ascorbate peroxidase enzyme activities, proline, and chemical composition as well as a rise in hydrogen peroxide and lipid peroxidation due to the limited availability of water in the maternal plant environment. On the other hand, providing adequate nutrition in the maternal plant environment resulted in improved germination index, increased starch, and oil content, as well as higher levels of nitrogen and phosphorus in the offspring of both Lallemantia species. Compared to the offspring of L. royleana, the offspring of L. iberica had a higher number of achenes, seeds, seed weight, larger seed size, greater germination index, and higher levels of starch, oil, nitrogen, phosphorus, potassium, and calcium. In contrast, the offspring of L. royleana exhibited higher longevity, enhanced germination under osmotic and salinity stress, increased proline levels, and higher activities of antioxidant enzymes such as superoxide dismutase, catalase, and ascorbic peroxidase as well as sucrose and total soluble sugar. The study concludes that the best seed performance, antioxidant enzyme activities, and carbohydrate levels were observed in the offspring of both Lallemantia species produced under 60 % soil available water depletion with AMF inoculation in the maternal plant environment. These findings highlight the significant impact of the soil available water depletion and AMF inoculation on the seed performance, physio-biochemical properties, and chemical composition of the offspring, providing valuable insights for optimizing seed production and performance.

Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating OsGA2ox7 in rice

Soil salinity has a major impact on rice seed germination, severely limiting rice production. Herein, a rice germination defective mutant under salt stress (gdss) was identified by using chemical mutagenesis. The GDSS gene was detected via MutMap and shown to encode potassium transporter OsHAK9. Phenotypic analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt stress. OsHAK9 is highly expressed in germinating seed embryos. Ion contents and non-invasive micro-test technology results showed that OsHAK9 restricted K+ efflux in salt-exposed germinating seeds for the balance of K+/Na+. Disruption of OsHAK9 significantly reduced gibberellin 4 (GA4) levels, and the germination defective phenotype of oshak9a was partly rescued by exogenous GA3 treatment under salt stress. RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress, and the expression of OsGA2ox7 was significantly inhibited by salt stress. Null mutants of OsGA2ox7 created using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt stress. Overall, our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7, which provides a novel clue about the relationship between GA and OsHAKs in rice.

Polylactic acid microplastics have stronger positive effects on the qualitative traits of rice (Oryza sativa L.) than polyethylene microplastics: Evidence from a simulated field experiment

Soil pollution by microplastics (MPs) from different types of agricultural films has received substantial attention due to its potential effects on crop quality. To date, the effects of different types of MPs on rice grain quality and their underlying molecular mechanisms have not been clarified. In this study, we examined the effects of polyethylene MPs (PE-MPs) and biodegradable polylactic acid MPs (PLA-MPs) on rice grain quality at the environmental level (0.5 %) and evaluated the molecular mechanism through transcriptome analysis. PE- and PLA-MPs increased the number of rice grains per plant by 19.83 % and 24.66 %, respectively, and decreased the rice empty-shell rate by 55.89 % and 26.53 %, respectively. However, PLA-MPs increased the 1000-seed weight by 11.37 %, whereas PE-MPs had no obvious impact in this respect. Furthermore, MP exposure, especially that of PE-MPs, affected the content of mineral elements, fatty acids, and amino acids of rice grains by disturbing the expression of genes related to these functions and metabolism. Our findings provide insights into the response of rice grains to the stress caused by different MPs.

Cadmium accumulation dynamics in the rice endosperm during grain filling revealed by autoradiography

Cadmium (Cd) is one of the environmental pollutants contaminated in our food. Several previous reports showed that rice polishing cannot be efficient to reduce Cd content in white rice, implying the characteristic Cd distribution in rice grain. However, Cd distribution has not been fully elucidated so far. Herein, 109Cd radiotracer experiment was performed using the rice seedlings at various time points after flowering to obtain autoradiographs of the brown rice to visually understand the Cd transport and distribution during the grain-filling process. It was shown that 109Cd accumulated in the outermost area of the brown rice, and also in the middle part of the starchy endosperm, resulting in the appearance of the double circle distribution pattern, which was not observed in the autoradiographs of 65Zn. The inner circle of 109Cd located around the center of the endosperm was developed particularly at around 8 and 10 days after flowering. After this period, 109Cd started to deposit at the outer part of the endosperm, which was also found in the autoradiograph of 14C-sucrose. Considering the physiology of grain development, the contribution of water transport and protein synthesis in the endosperm on the characteristic Cd distribution pattern was hypothesized.

Effects of soil amendments on Cd and As mobility in the soil-rice system and their distribution in the grain

The accumulation, mobilization, and distribution of toxic metal(loid)s in rice are key factors that affect food security and determine bio-utilization patterns. In this study, five soil amendments with different components were used in paddy fields to study the key factors: organic amendments: (1) polyaspartic acid (OA1) and (2) organic fertilizer (OA2); inorganic amendments: (3) kaolinite (IA1) and (4) magnesium slag (IA2); and organic-inorganic composite amendments: (5) modified biochar/quicklime (OIA). Although the Cd and As exhibited opposite chemical dissolution behaviors, IA1/OIA, can simultaneously reduce their accumulation and transfer coefficients in rice tissues, while other amendments only work for one of them. The in situ distribution in grains showed that IA1/OIA changed the original Cd distribution in the lemma and palea, whereas all amendments reduced Cd accumulation in the germ. In contrast, OA1/IA2 amendments led to more As accumulation in the rice husks and bran than in the endosperm center, and the germ had higher As signals. Because of their similar transport pathways and interactions, the concentrations of Cd and As in the grains were correlated with a variety of mineral elements (Fe, Mo, Zn, etc.). Changes in the Cd/As concentration and distribution in rice were achieved through the improvement of soil properties and plant growth behavior through amendments. The application of OIA resulted in the highest immobilization indices, at 82.17 % and 35.34 % for Cd and As, respectively. The Cd/As concentrations in the rice grains were highly positively correlated with extractable-Cd/As in the soil (Cd: R2 = 0.95, As: R2 = 0.93). These findings reveal the migration and distribution mechanisms of Cd and As in the soil-rice system, and thus provide fundamental information for minimizing food safety risk.

Agronomic and ionomics indicators of high-yield, mineral-dense, and low-Cd grains of wheat (Triticum aestivum L.) cultivars

The accumulation of toxic and essential nutrient elements in wheat grain influences wheat yield, grain nutritional quality, and human health. Here, we assessed the potential for breeding wheat cultivars to combine high yield with low cadmium and high iron and/or zinc concentrations in grains, and we screened appropriate cultivars. A pot experiment was conducted to explore differences in grain cadmium, iron, and zinc concentrations among 68 wheat cultivars, as well as their relationships with other nutrient elements and agronomic characters. The results showed 2.04-, 1.71-, and 1.64-fold differences in grain cadmium, iron, and zinc concentrations, respectively, among the 68 cultivars. Grain cadmium concentration was positively correlated with grain zinc, iron, magnesium, phosphorus, and manganese concentrations. Grain copper concentration was positively correlated with grain zinc and iron concentrations, but not with grain cadmium concentration. Therefore, copper has a potential role in regulating grain iron and zinc accumulation without influencing cadmium concentration in wheat grain. There were no significant relationships between grain cadmium concentration and four important wheat agronomic characters (i.e., grain yield, straw yield, thousand kernel weight, and plant height), indicating that the breeding of low-cadmium-accumulating cultivars with dwarfism and high yield characteristics is possible. On cluster analysis, four cultivars (Ningmai11, Xumai35, Baomai6, and Aikang58) exhibited low-cadmium and high-yield characteristics. Among them, Aikang58 contained moderate iron and zinc concentrations, while Ningmai11 had relatively high iron but low zinc concentrations in the grain. These results imply that it is feasible to breed high-yield dwarf wheat with low cadmium and moderate iron and zinc concentrations in the grain.

Comprehensive analysis of physiological and metabolomic responses to drought reveals specific modulation of acquired tolerance mechanisms in rice

Mild stresses induce "acquired tolerance traits" (ATTs) that provide tolerance when stress becomes severe. Here, we identified the genetic variability in ATTs among a panel of rice germplasm accessions and demonstrated their relevance in protecting growth and productivity under water-limited conditions. Diverse approaches, including physiological screens, association mapping and metabolomics, were adopted and revealed 43 significant marker-trait associations. Nontargeted metabolomic profiling of contrasting genotypes revealed 26 "tolerance-related-induced" primary and secondary metabolites in the tolerant genotypes (AC-39000 and AC-39020) compared to the susceptible one (BPT-5204) under water-limited condition. Metabolites that help maintain cellular functions, especially Calvin cycle processes, significantly accumulated more in tolerant genotypes, which resulted in superior photosynthetic capacity and hence water use efficiency. Upregulation of the glutathione cycle intermediates explains the ROS homeostasis among the tolerant genotypes, maintaining spikelet fertility, and grain yield under stress. Bioinformatic dissection of a major effect quantitative trait locus on chromosome 8 revealed genes controlling metabolic pathways leading to the production of osmolites and antioxidants, such as GABA and raffinose. The study also led to the identification of specific trait donor genotypes that can be effectively used in translational crop improvement activities.