Robust identification of low-Cd rice varieties by boosting the genotypic effect of grain Cd accumulation in combination with marker-assisted selection

Genomic prediction for agronomic traits in a diverse Flax (Linum usitatissimum L.) germplasm collection

Breeding programs require exhaustive phenotyping of germplasms, which is time-demanding and expensive. Genomic prediction helps breeders harness the diversity of any collection to bypass phenotyping. Here, we examined the genomic prediction's potential for seed yield and nine agronomic traits using 26,171 single nucleotide polymorphism (SNP) markers in a set of 337 flax (Linum usitatissimum L.) germplasm, phenotyped in five environments. We evaluated 14 prediction models and several factors affecting predictive ability based on cross-validation schemes. Models yielded significant variation among predictive ability values across traits for the whole marker set. The ridge regression (RR) model covering additive gene action yielded better predictive ability for most of the traits, whereas it was higher for low heritable traits by models capturing epistatic gene action. Marker subsets based on linkage disequilibrium decay distance gave significantly higher predictive abilities to the whole marker set, but for randomly selected markers, it reached a plateau above 3000 markers. Markers having significant association with traits improved predictive abilities compared to the whole marker set when marker selection was made on the whole population instead of the training set indicating a clear overfitting. The correction for population structure did not increase predictive abilities compared to the whole collection. However, stratified sampling by picking representative genotypes from each cluster improved predictive abilities. The indirect predictive ability for a trait was proportionate to its correlation with other traits. These results will help breeders to select the best models, optimum marker set, and suitable genotype set to perform an indirect selection for quantitative traits in this diverse flax germplasm collection.

Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice

Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.

Rapid identification of high and low cadmium (Cd) accumulating rice cultivars using machine learning models with molecular markers and soil Cd levels as input data

Excessive accumulation of cadmium (Cd) in rice grains threatens food safety and human health. Growing low Cd accumulating rice cultivars is an effective approach to produce low-Cd rice. However, field screening of low-Cd rice cultivars is laborious, time-consuming, and subjected to the influence of environment × genotype interactions. In the present study, we investigated whether machine learning-based methods incorporating genotype and soil Cd concentration can identify high and low-Cd accumulating rice cultivars. One hundred and sixty-seven locally adapted high-yielding rice cultivars were grown in three fields with different soil Cd levels and genotyped using four molecular markers related to grain Cd accumulation. We identified sixteen cultivars as stable low-Cd accumulators with grain Cd concentrations below the 0.2 mg kg^-1 food safety limit in all three paddy fields. In addition, we developed eight machine learning-based models to predict low- and high-Cd accumulating rice cultivars with genotypes and soil Cd levels as input data. The optimized model classifies low- or high-Cd cultivars (i.e., the grain Cd concentration below or above 0.2 mg kg^-1) with an overall accuracy of 76%. These results indicate that machine learning-based classification models constructed with molecular markers and soil Cd levels can quickly and accurately identify the high- and low-Cd accumulating rice cultivars.

Cadmium Absorption in Various Genotypes of Rice under Cadmium Stress

Cadmium (Cd) is a kind of heavy metal. Cadmium pollution in paddy fields will accumulate a large amount of cadmium in rice, which will affect the growth and development of rice. In addition, long-term consumption of rice contaminated with Cd can harm human health. In this study, four rice varieties with high Cd accumulation (S4699, TLY619, JHY1586, QLY155) and four varieties with low Cd accumulation (YY4949, CYJ-7, G8YXSM, MXZ-2) were screened through field experiments for two consecutive years (2021 and 2022) and differences in antioxidant enzyme systems and expression of genes in their organs were analyzed. The total Cd content showed as follows: indica rice > japonica rice, high-Cd-accumulation variety > low-Cd-accumulation variety, and the total Cd content of each organ of rice showed root > stem > leaf > grain. The results of the antioxidant enzyme system showed that the contents of malondialdehyde (MAD), reduced glutathione (GSH), oxidized glutathione (GSSH), and peroxidase (POD) were positively correlated with the total Cd content in rice, and superoxide dismutase (SOD) showed the opposite performance in the leaves. There was no correlation between catalase (CAT) and Cd content, but CAT content decreased in leaves and grains and increased in roots and stems with increasing fertility. Based on this study, RT-qPCR was used to further validate the expression of Cd-uptake-related genes in different rice varieties. It was found that high expression of OsHMA3, OsCCX2, OsNRAMP5, and OsHMA9 genes promoted Cd uptake and translocation in rice, especially in rice varieties with high Cd accumulation. The high expression of OslRT1, OsPCR1, and OsMTP1 genes hindered Cd uptake by rice plants, which was especially evident in low-accumulating Cd rice varieties. These results provide an important theoretical reference and scientific basis for our in-depth study and understanding of the mechanism of cadmium stress tolerance in rice.

Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars

Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.

Identification of subspecies-divergent genetic loci responsible for mineral accumulation in rice grains

Rice (Oryza sativa L.) is a major staple food that provides not only dietary calories but also trace elements for the global inhabitants. The insufficiency of mineral nutrients and the potential accumulation of excessive toxic elements in grains pose risks to human health. The substantial natural variations in mineral accumulation in rice grains presents potentials for genetic improvements of rice via biofortifications of essential mineral nutrients and eliminations of toxic elements in grains. However, the genetic mechanisms underlying the natural variations in mineral accumulation have not been fully explored to date owing to unstable phenotypic variations, which are attributed to poor genetic performance and strong environmental effects. In this study, we first compared the genetic performance of different normalization approaches in determining the grain-Cd, grain-Mn, and grain-Zn variations in rice in different genetic populations. Then through quantitative trait loci (QTLs) identification in two rice inter-ectype populations, three QTLs, including qCd7, qMn3, and qZn7, were identified and the QTLs were found to exhibit allelic differentiation in the different ecotypes. Our results were expected to broaden our understanding for mineral accumulation in rice and propose the potential functional alleles that can be explored for further genetic improvement of rice.

Recruitment of specific microbes through exudates affects cadmium activation and accumulation in Brassica napus

Exploration of the mechanisms of cadmium (Cd) activation mediated by the rhizosphere process is important to advance our understanding of Cd accumulation in plants. In this study, two oilseed rape cultivars (L338, L351) with varied Cd accumulation traits were applied and the responses of their rhizosphere ecology to Cd stress were investigated by metabolome and microbiome. The results showed that shoot Cd accumulations in L338 accounted for 54.16% and 64.76% of those in L351 under low and high Cd contamination, respectively. Moreover, the cultivars response of rhizosphere process reflected that the lower pH and higher Cd mobility were assigned to the characters of L351, which were induced by the secretion of carboxylic acid (e.g. Acetaminophen cysteine, N-Fructosyl alliin) and the enrichment of bacterial taxa with the capacities of Cd resistant and activation (e.g. Sphingomonas, Flavobacterium, Neorhizobium, Altererythrobacter). Conclusively, the varied Cd accumulation traits of two oilseed rape cultivars were not only derived from the Cd transfer ability, it would be ascribed to Cd mobility regulated by rhizosphere processes as well. The results provide baseline data and a new perspective on the cultivar response of Cd accumulation, thus maintaining cleaner production of oilseed rape.

Interplanting of rice cultivars with high and low Cd accumulation can achieve the goal of "repairing while producing" in Cd-contaminated soil

Interplanting has been highlighted as a promising, cost-effective, and environmentally friendly solution for the remediation of contaminated soil. In this study, field experiments were conducted to study growth and cadmium (Cd) uptake in monoculture and interplanting systems with rice varieties Changliangyou 772 (C-772) and Changxianggu (Cho-ko-koku). And a pot culture experiment was conducted to investigate the response of the rhizosphere microecology of these two rice varieties. In the interplanting system of the field study, the Cd concentration in the grains of C-772 was significantly reduced (P < 0.05) from 0.30 mg kg^-1 to 0.16 mg kg^-1 and reached the national food safety standard of China (GB2762-2017, 0.20 mg kg^-1), whereas the bioconcentration amount (BCA) per plant of Cd in Cho-ko-koku was significantly increased by 68.18 % (P < 0.05). The land equivalent ratio (LER) and Cd metal removal equivalent ratio (MRER) of the interplanting system were 1.03 and 1.05, illustrating that the interplanting system was superior in terms of yield and Cd elimination. In the pot experiment, the interplanting system significantly (P < 0.05) reduced the iron plaque content on the root surface and organic acids content in the rhizosphere environment of C-772 while markedly increasing those levels in Cho-ko-koku. At ripening stage, the interplanting system significantly decreased the rhizosphere available Cd concentration of C-772 from 0.38 mg kg^-1 to 0.22 mg kg^-1 (P < 0.05), while significantly increased the rhizosphere available Cd concentration of Cho-ko-koku from 0.27 mg kg^-1 to 0.32 mg kg^-1 (P < 0.05). Thus, Cd uptake of C-772 and Cho-ko-koku showed apparent differences. Oxalic and tartaric acid were identified as the most crucial factors affecting Cd uptake by C-772 and Cho-ko-koku in the interplanting system, respectively. In summary, this interplanting system is a promising planting pattern that can simultaneously improve land use efficiency and alleviate Cd pollution.

Capture Mechanism of Cadmium in Agricultural Soil Via Iron-Modified Graphene

Cadmium (Cd) contamination in agricultural soils has caused extensive concern to researchers. Biochar with iron-compound modifications could give rise to the synergistic effect for Cd restriction. However, the related capture mechanism based on physicochemical properties is unclear. In this study, first principles calculations are proposed to explore the adsorption ability and potential mechanism of the ferric hydroxide modified graphene (Fe@G) for capturing CdCl2. The simulation results show that the adsorption energy to CdCl2 could enhance to −1.60 eV when Fe(OH)3 is introduced on graphene. Subsequently, analyses of electronic properties demonstrated a significant electron transfer between Cd s-orbital and O p-orbital, thereby leading to strong adsorption energy. This theoretical study not only identifies a powerful adsorption material for Cd reduction in agricultural soils and reveals the capture mechanism of Fe@G for Cd but also provides a foundation and strategy for Cd reduction in agricultural soils.

Effects of Red Mud on Cadmium Uptake and Accumulation by Rice and Chemical Changes in Rhizospheres by Rhizobox Method

Red mud (RM), a byproduct of aluminum production, is used as amendments to increase the pH and reduce the available Cd in soil, but the effects of RM treatments on rice and rhizosphere chemistry changes at different radial-oxygen-loss (ROL) rates and developmental stages remain unclear. To address this concern, a rhizobox trial was conducted to investigate the effect of 0%, 0.5%, and 1.0% RM, on Cd accumulation by rice cultivars differing in ROL rate (‘Zheyou12’ (ZY12), ‘Qianyou1’ (QY1), and ‘Chunjiangnuo2’ (CJN2)) at two growth stages (tillering and bolting). The results showed that mobility factors of Cd in the soil were decreased significantly at both stages. The Cd mobility factor (MF) of CJN2 was decreased by 33.01% under 1% RM treatment at bolting stage. The pH value was increased by 0.39–0.53 units at two stages. RM contains large amounts of metals, which can increase soil iron (Fe) and manganese (Mn) concentrations, reduce redox potential, and transform the available Cd into Fe/Mn oxide-bound Cd. In addition, the Fe plaque further increased to inhibit the transformation of Cd. These changes reduced the available Cd in the soil and further decreased Cd absorption by rice. With the increase in RM concentration, the shoot and root biomass increased, and Cd accumulation in the plant significantly decreased. Compared with that under 0% RM treatment, the shoot Cd concentrations of ZY12, QY1, and CJN2 under 1% RM treatment at the bolting stage decreased by 27.59%, 36.00%, and 46.03%, respectively. The relative Cd accumulation ability of the three rice cultivars was CJN2 < QY1 < ZY12. The ROL promotes Fe plaque formation on the root surface. The Fe plaque is an obstacle or buffer between Cd and rice, which can immobilize Cd in Fe plaque and further reduce Cd absorption by rice. The addition of RM, in combination with a high-ROL rice cultivar, is a potential strategy for the safe production of rice on Cd-contaminated soils.

CF1 reduces grain-cadmium levels in rice (Oryza sativa)

Rice (Oryza sativa) is a leading source of dietary cadmium (Cd), a non-essential heavy metal that poses a serious threat to human health. There are significant variations in grain-Cd levels in natural rice populations, which make the breeding of low-Cd rice a cost-effective way to mitigate grain-Cd accumulation. However, the genetic factors that regulate grain-Cd accumulation have yet to be fully established, thereby hindering the development of low-Cd varieties. Here, we reported a low-Cd quantitative trait locus, CF1, that has the potential to reduce Cd accumulation in rice grains. CF1 is allelic to the metal transporter OsYSL2, which transports Fe from the roots to the shoots. However, it is incapable of binding Cd, and thus, reduces grain-Cd levels indirectly rather than directly in the form of upward delivery. Further analysis showed that high expression levels of CF1 improve Fe nutrition in the shoots, subsequently inhibiting Cd uptake by systemically inhibiting expression of the main Cd uptake gene OsNramp5 in the roots. Compared with the CF1 allele from '02428' (CF1⁰²⁴²⁸ ), higher expression levels of CF1 from 'TQ' (CF1^TQ ) increased the Fe contents and decreased Cd levels in rice grains. In natural rice populations, CF1^TQ was found to be a minor allele, while CF1⁰²⁴²⁸ is present in most japonica rice, suggesting that CF1^TQ could be widely integrated into the japonica rice genome to generate low-Cd varieties. Overall, these results broaden our mechanistic understanding of the natural variation in grain-Cd accumulation, supporting marker-assisted selection of low-Cd rice.

Multidimensional Role of Silicon to Activate Resilient Plant Growth and to Mitigate Abiotic Stress

Sustainable agricultural production is critically antagonistic by fluctuating unfavorable environmental conditions. The introduction of mineral elements emerged as the most exciting and magical aspect, apart from the novel intervention of traditional and applied strategies to defend the abiotic stress conditions. The silicon (Si) has ameliorating impacts by regulating diverse functionalities on enhancing the growth and development of crop plants. Si is categorized as a non-essential element since crop plants accumulate less during normal environmental conditions. Studies on the application of Si in plants highlight the beneficial role of Si during extreme stressful conditions through modulation of several metabolites during abiotic stress conditions. Phytohormones are primary plant metabolites positively regulated by Si during abiotic stress conditions. Phytohormones play a pivotal role in crop plants' broad-spectrum biochemical and physiological aspects during normal and extreme environmental conditions. Frontline phytohormones include auxin, cytokinin, ethylene, gibberellin, salicylic acid, abscisic acid, brassinosteroids, and jasmonic acid. These phytohormones are internally correlated with Si in regulating abiotic stress tolerance mechanisms. This review explores insights into the role of Si in enhancing the phytohormone metabolism and its role in maintaining the physiological and biochemical well-being of crop plants during diverse abiotic stresses. Moreover, in-depth information about Si's pivotal role in inducing abiotic stress tolerance in crop plants through metabolic and molecular modulations is elaborated. Furthermore, the potential of various high throughput technologies has also been discussed in improving Si-induced multiple stress tolerance. In addition, a special emphasis is engrossed in the role of Si in achieving sustainable agricultural growth and global food security.