Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Using VIS-NIR hyperspectral imaging and deep learning for non-destructive high-throughput quantification and visualization of nutrients in wheat grains

High-throughput and low-cost quantification of the nutrient content in crop grains is crucial for food processing and nutritional research. However, traditional methods are time-consuming and destructive. A high-throughput and low-cost method of quantification of wheat nutrients with VIS-NIR (400-1700 nm) hyperspectral imaging is proposed in this study. Stepwise linear regression (SLR) was used to predict hundreds of nutrients accurately (R2 > 0.6); results improved when the hyperspectral data was processed with the first derivative. Knockout materials were also used to verify their practical application value. Various nutrients' characteristic wavelengths were mainly concentrated in the visible regions of 400-500 nm and 900-1000 nm. Finally, we proposed an improved pix2pix conditional generative network model to visualize the nutrients distribution and showed better results compared with the original. This research highlights the potential of hyperspectral technology in high-throughput and non-destructive determination and visualization of grain nutrients with deep learning.

OsCOPT7 is involved in copper accumulation and transport through xylem

Copper (Cu) is an essential micronutrient for humans, but excessive Cu in rice grains causes health risks. Currently, the mechanisms underlying Cu accumulation in rice are unclear. Here, we identified a novel member of the high-affinity copper transporter (Ctr)-like (COPT) protein family in rice, OsCOPT7, which controls Cu accumulation in rice grains. Mutation in the coding sequence of OsCOPT7 (mutant lc1) leads to inhibition of Cu transport through the xylem, contributing to lower Cu concentrations in the grain of lc1. Knockout or modulation of the expression of OsCOPT7 significantly impacts Cu transportation in the xylem and its accumulation in rice grains. OsCOPT7 localizes at the multi-pass membrane in the cell and the gene is expressed in the exodermis and stele cells, facilitating Cu loading into the xylem. OsCOPT7 expression is upregulated under Cu deficiency and in various organs, implying its contribution to Cu distribution within the rice plant. The variable expression pattern of OsCOPT7 suggests that OsCOPT7 expression responds to Cu stress in rice. Moreover, assays reveal that OsCOPT7 expression level is suppressed by the SQUAMOSA promoter-binding protein-like 9 (OsSPL9) and that OsCOPT7 interacts with Antioxidant Protein1 (OsATX1). This study elucidates the involvement of OsCOPT7 in Cu loading into the xylem, its subsequent distribution within the rice plant, and the potential of this protein in reducing the risk of high Cu concentrations in rice grain grown on Cu-contaminated soil.

Genome-wide association study of trace elements in maize kernels

Maize (Zea mays L.), a staple food and significant economic crop, is enriched with riboflavin, micronutrients and other compounds that are beneficial for human health. As emphasis on the nutritional quality of crops increases maize research has expanded to focus on both yield and quality. This study exploreed the genetic factors influencing micronutrient levels in maize kernels through a comprehensive genome-wide association study (GWAS). We utilized a diverse panel of 244 inbred maize lines and approximately 3 million single nucleotide polymorphisms (SNPs) to investigate the accumulation of essential and trace elements including cadmium (Cd), cobalt (Co), copper (Cu), nickel (Ni), selenium (Se) and zinc (Zn). Our analysis identified 842 quantitative trait loci (QTLs), with 12 QTLs shared across multiple elements and pinpointed 524 potential genes within a 100 kb radius of these QTLs. Notably ZmHMA3 has emerged as a key candidate gene previously reported to influence the Cd accumulation. We highlighted ten pivotal genes associated with trace element transport including those encoding heavy metal ATPases, MYB transcription factors, ABC transporters and other crucial proteins involved in metal handling. Additionally, haplotype analysis revealed that eight inbred linesaccumulated relatively high levels of beneficial elements while harmful elements were minimized. These findings elucidate the genetic mechanisms underlying trace element accumulation in maize kernels and provide a foundation for the breeding of nutritionally enhanced maize varieties.

Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica)

KEY MESSAGE

One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.

Genetic background influences mineral accumulation in rice straw and grains under different soil pH conditions

Mineral element accumulation in plants is influenced by soil conditions and varietal factors. We investigated the dynamic accumulation of 12 elements in straw at the flowering stage and in grains at the mature stage in eight rice varieties with different genetic backgrounds (Japonica, Indica, and admixture) and flowering times (early, middle, and late) grown in soil with various pH levels. In straw, Cd, As, Mn, Zn, Ca, Mg, and Cu accumulation was influenced by both soil pH and varietal factors, whereas P, Mo, and K accumulation was influenced by pH, and Fe and Ni accumulation was affected by varietal factors. In grains, Cd, As, Mn, Cu, Ni, Mo, Ca, and Mg accumulation was influenced by both pH and varietal factors, whereas Zn, Fe, and P accumulation was affected by varietal factors, and K accumulation was not altered. Only As, Mn, Ca and Mg showed similar trends in the straw and grains, whereas the pH responses of Zn, P, K, and Ni differed between them. pH and flowering time had synergistic effects on Cd, Zn, and Mn in straw and on Cd, Ni, Mo, and Mn in grains. Soil pH is a major factor influencing mineral uptake in rice straw and grains, and genetic factors, flowering stage factors, and their interaction with soil pH contribute in a combined manner.

Iron-modified biochar inhibiting Cd uptake in rice by Cd co-deposition with Fe oxides in the rice rhizosphere

Fe-enriched biochar has proven to be effective in reducing Cd uptake in rice plants by enhancing iron plaque formation. However, the effect of Fe on biochar, especially the biochar with high S content, for Cd immobilization in rice rhizosphere was not fully understood. To obtain eco-friendly Fe-loaded biochar at a low cost, garlic straw, bean straw, and rape straw were chosen as the feedstocks for Fe-enhanced biochar production by co-pyrolysis with Fe2O3. The resulting biochars and Fe-loaded biochars were GBC, BBC, BRE, GBC-Fe, BBC-Fe, and BRE-Fe, respectively. XRD and FTIR analyses showed that Fe was successfully loaded onto the biochar. The pristine and Fe-containing biochars were applied at rates of 0% (BC0) and 0.1% in pot experiments. Results suggested that BBC-Fe caused the highest reduction in Cd content of rice grain, and the reductions were 67.9% and 31.4%, compared with BC0 and BBC, respectively. Compared to BBC, BBC-Fe effectively reduced Cd uptake in rice roots by 47.5%. The exchangeable and acid-soluble fraction of Cd (F1-Cd) in soil with BBC-Fe treatment was 37.6% and 63.7% lower than that of BC0 and BBC, respectively. Compared to BC0, soil pH was increased by 0.53 units with BBC-Fe treatment. BBC-Fe significantly increased Fe oxides (free Fe oxides, amorphous Fe oxides, and complex Fe oxides) content in the soil as well. DGT study demonstrated that BBC-Fe could enhance the mobility of sulfate in the rhizosphere, which might be beneficial for Cd fixation in the rhizosphere. Moreover, BBC-Fe increased the relative abundance of Bacteroidota, Firmicutes, and Clostridia, which might be beneficial for Cd immobilization in the rhizosphere. This work highlights the synergistic effect of loaded Fe and biochar on Cd immobilization by enhancing Cd deposited with Fe oxides.

The differences in metabolites, starch structure, and physicochemical properties of rice were related to the decrease in taste quality under high nitrogen fertilizer application

Nitrogen fertilizer application is one of the key cultivation practices to improve rice yields. However, the application of high nitrogen fertilizers often leads to a reduction in the stickiness of the rice after cooking, thus reducing the taste quality of rice. Moreover, there are differences in taste quality among rice varieties, and the mechanism has not been studied in depth. In this study, two rice varieties (Meixiangzhan2hao and Exiang2hao) were planted under two nitrogen fertilizer levels. The physicochemical properties and taste quality of the rice were determined after maturity. Our results showed that high nitrogen fertilizer level alters tryptophan metabolism in rice, increasing most amino acid content and protein content in rice. The high content of protein and the higher short-range ordered structure of starch inhibited the gelatinization characteristics of starch and reduced the taste quality of rice. Under high nitrogen fertilizer application, Exiang2hao showed smaller increases in protein content, lower level of amylose and relative crystallinity, and higher content of lipid metabolites. These differences in chemical substances resulted in a less pronounced reduction in the taste quality of Exiang2hao. In this study, the taste quality of different rice varieties under different levels of nitrogen fertilizer application was analyzed, providing new ideas for future improvement of rice taste quality.

Machine learning applications to improve flavor and nutritional content of horticultural crops through breeding and genetics

Over the last decades, significant strides were made in understanding the biochemical factors influencing the nutritional content and flavor profile of fruits and vegetables. Product differentiation in the produce aisle is the natural consequence of increasing consumer power in the food industry. Cotton-candy grapes, specialty tomatoes, and pineapple-flavored white strawberries provide a few examples. Given the increased demand for flavorful varieties, and pressing need to reduce micronutrient malnutrition, we expect breeding to increase its prioritization toward these traits. Reaching this goal will, in part, necessitate knowledge of the genetic architecture controlling these traits, as well as the development of breeding methods that maximize their genetic gain. Can artificial intelligence (AI) help predict flavor preferences, and can such insights be leveraged by breeding programs? In this Perspective, we outline both the opportunities and challenges for the development of more flavorful and nutritious crops, and how AI can support these breeding initiatives.

Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis

KEY MESSAGE

This study provided important insights into the genetic architecture of variations in A. thaliana leaf ionome in a cell-type-specific manner. The functional interpretation of traits associated variants by expression quantitative trait loci (eQTL) analysis is usually performed in bulk tissue samples. While the regulation of gene expression is context-dependent, such as cell-type-specific manner. In this study, we estimated cell-type abundances from 728 bulk tissue samples using single-cell RNA-sequencing dataset, and performed cis-eQTL mapping to identify cell-type-interaction eQTL (cis-eQTLs(ci)) in A. thaliana. Also, we performed Genome-wide association studies (GWAS) analyses for 999 accessions to identify the genetic basis of variations in A. thaliana leaf ionome. As a result, a total of 5,664 unique eQTL genes and 15,038 unique cis-eQTLs(ci) were significant. The majority (62.83%) of cis-eQTLs(ci) were cell-type-specific eQTLs. Using colocalization, we uncovered one interested gene AT2G25590 in Phloem cell, encoding a kind of plant Tudor-like protein with possible chromatin-associated functions, which colocalized with the most significant cis-eQTL(ci) of a Mo-related locus (Chr2:10,908,806:A:C; P = 3.27 × 10-27). Furthermore, we prioritized eight target genes associated with AT2G25590, which were previously reported in regulating the concentration of Mo element in A. thaliana. This study revealed the genetic regulation of ionomic variations and provided a foundation for further studies on molecular mechanisms of genetic variants controlling the A. thaliana ionome.

Plant genome resequencing and population genomics: Current status and future prospects

Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.

Estimating nutrient concentrations and uptake in rice grain in sub-Saharan Africa using linear mixed-effects regression

Context or problem

Quantification of nutrient concentrations in rice grain is essential for evaluating nutrient uptake, use efficiency, and balance to develop fertilizer recommendation guidelines. Accurate estimation of nutrient concentrations without relying on plant laboratory analysis is needed in sub-Saharan Africa (SSA), where farmers do not generally have access to laboratories.

Objective or research question

The objectives are to 1) examine if the concentrations of macro- (N, P, K, Ca, Mg, S) and micronutrients (Fe, Mn, B, Cu) in rice grain can be estimated using agro-ecological zones (AEZ), production systems, soil properties, and mineral fertilizer application (N, P, and K) rates as predictor variables, and 2) to identify if nutrient uptakes estimated by best-fitted models with above variables provide improved prediction of actual nutrient uptakes (predicted nutrient concentrations x grain yield) compared to average-based uptakes (average nutrient concentrations in SSA x grain yield).

Methods

Cross-sectional data from 998 farmers' fields across 20 countries across 4 AEZs (arid/semi-arid, humid, sub-humid, and highlands) in SSA and 3 different production systems: irrigated lowland, rainfed lowland, and rainfed upland were used to test hypotheses of nutrient concentration being estimable with a set of predictor variables among above-cited factors using linear mixed-effects regression models.

Results

All 10 nutrients were reasonably predicted [Nakagawa's R² ranging from 0.27 (Ca) to 0.79 (B), and modeling efficiency ranging from 0.178 (Ca) to 0.584 (B)]. However, only the estimation of K and B concentrations was satisfactory with a modeling efficiency superior to 0.5. The country variable contributed more to the variation of concentrations of these nutrients than AEZ and production systems in our best predictive models. There were greater positive relationships (up to 0.18 of difference in correlation coefficient R) between actual nutrient uptakes and model estimation-based uptakes than those between actual nutrient uptakes and average-based uptakes. Nevertheless, only the estimation of B uptake had significant improvement among all nutrients investigated.

Conclusions

Our findings suggest that with the exception of B associated with high model EF and an improved uptake over the average-based uptake, estimates of the macronutrient and micronutrient uptakes in rice grain can be obtained simply by using average concentrations of each nutrient at the regional scale for SSA.

Implications

Further investigation of other factors such as the timing of fertilizer applications, rice variety, occurrence of drought periods, and atmospheric CO₂ concentration is warranted for improved prediction accuracy of nutrient concentrations.

Magnesium supply alleviates iron toxicity-induced leaf bronzing in rice through exclusion and tissue-tolerance mechanisms

Introduction

Iron (Fe) toxicity is a widespread nutritional disorder in lowland rice causing growth retardation and leaf symptoms referred to as leaf bronzing. It is partly caused by an imbalance of nutrients other than Fe and supply of these is known to mitigate the toxicity. But the physiological and molecular mechanisms involved are unknown.

Methods

We investigated the effect of magnesium (Mg) on Fe toxicity tolerance in a field study in the Central Highlands of Madagascar and in hydroponic experiments with excess Fe (300 mg Fe L-1). An RNA-seq analysis was conducted in a hydroponic experiment to elucidate possible mechanisms underlying Mg effects.

Results and discussion

Addition of Mg consistently decreased leaf bronzing under both field and hydroponic conditions, whereas potassium (K) addition caused minor effects. Plants treated with Mg tended to have smaller shoot Fe concentrations in the field, suggesting enhanced exclusion at the whole-plant level. However, analysis of multiple genotypes showed that Fe toxicity symptoms were also mitigated without a concomitant decrease of Fe concentration, suggesting that increased Mg supply confers tolerance at the tissue level. The hydroponic experiments also suggested that Mg mitigated leaf bronzing without significantly decreasing Fe concentration or oxidative stress as assessed by the content of malondialdehyde, a biomarker for oxidative stress. An RNA-seq analysis revealed that Mg induced more changes in leaves than roots. Subsequent cis-element analysis suggested that NAC transcription factor binding sites were enriched in genes induced by Fe toxicity in leaves. Addition of Mg caused non-significant enrichment of the same binding sites, suggesting that NAC family proteins may mediate the effect of Mg. This study provides clues for mitigating Fe toxicity-induced leaf bronzing in rice.

A vacuolar transporter plays important roles in zinc and cadmium accumulation in rice grain

Rice grain is a poor dietary source of zinc (Zn) but the primary source of cadmium (Cd) for humans; however, the molecular mechanisms for their accumulation in rice grain remain incompletely understood. This study functionally characterized a tonoplast-localized transporter, OsMTP1. OsMTP1 was preferentially expressed in the roots, aleurone layer, and embryo of seeds. OsMTP1 knockout decreased Zn concentration in the root cell sap, roots, aleurone layer and embryo, and subsequently increased Zn concentration in shoots and polished rice (endosperm) without yield penalty. OsMTP1 haplotype analysis revealed elite alleles associated with increased Zn level in polished rice, mostly because of the decreased OsMTP1 transcripts. OsMTP1 expression in yeast enhanced Zn tolerance but did not affect that of Cd. While OsMTP1 knockout resulted in decreased uptake, translocation and accumulation of Cd in plant and rice grain, which could be attributed to the indirect effects of altered Zn accumulation. Our results suggest that rice OsMTP1 primarily functions as a tonoplast-localized transporter for sequestrating Zn into vacuole. OsMTP1 knockout elevated Zn concentration but prevented Cd deposition in polished rice without yield penalty. Thus, OsMTP1 is a candidate gene for enhancing Zn level and reducing Cd level in rice grains.

The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement

Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.

Heavy metals and arsenic stress in food crops: Elucidating antioxidative defense mechanisms in hyperaccumulators for food security, agricultural sustainability, and human health

The spread of heavy metal(loid)s at soil-food crop interfaces has become a threat to sustainable agricultural productivity, food security, and human health. The eco-toxic effects of heavy metals on food crops can be manifested through reactive oxygen species that have the potential to disturb seed germination, normal growth, photosynthesis, cellular metabolism, and homeostasis. This review provides a critical overview of stress tolerance mechanisms in food crops/hyperaccumulator plants against heavy metals and arsenic (HM-As). The HM-As antioxidative stress tolerance in food crops is associated with changes in metabolomics (physico-biochemical/lipidomics) and genomics (molecular level). Furthermore, HM-As stress tolerance can occur through plant-microbe, phytohormone, antioxidant, and signal molecule interactions. Information regarding the avoidance, tolerance, and stress resilience of HM-As should help pave the way to minimize food chain contamination, eco-toxicity, and health risks. Advanced biotechnological approaches (e.g., genome modification with CRISPR-Cas9 gene editing) in concert with traditional sustainable biological methods are useful options to develop 'pollution safe designer cultivars' with increased climate change resilience and public health risks mitigation. Further, the usage of HM-As tolerant hyperaccumulator biomass in biorefineries (e.g., environmental remediation, value added chemicals, and bioenergy) is advocated to realize the synergy between biotechnological research and socio-economic policy frameworks, which are inextricably linked with environmental sustainability. The biotechnological innovations, if directed toward 'cleaner climate smart phytotechnologies' and 'HM-As stress resilient food crops', should help open the new path to achieve sustainable development goals (SDGs) and a circular bioeconomy.

Molecular membrane separation: plants inspire new technologies

Plants draw up their surrounding soil solution to gain water and nutrients required for growth, development and reproduction. Obtaining adequate water and nutrients involves taking up both desired and undesired elements from the soil solution and separating resources from waste. Desirable and undesirable elements in the soil solution can share similar chemical properties, such as size and charge. Plants use membrane separation mechanisms to distinguish between different molecules that have similar chemical properties. Membrane separation enables distribution or retention of resources and efflux or compartmentation of waste. Plants use specialised membrane separation mechanisms to adapt to challenging soil solution compositions and distinguish between resources and waste. Coordination and regulation of these mechanisms between different tissues, cell types and subcellular membranes supports plant nutrition, environmental stress tolerance and energy management. This review considers membrane separation mechanisms in plants that contribute to specialised separation processes and highlights mechanisms of interest for engineering plants with enhanced performance in challenging conditions and for inspiring the development of novel industrial membrane separation technologies. Knowledge gained from studying plant membrane separation mechanisms can be applied to developing precision separation technologies. Separation technologies are needed for harvesting resources from industrial wastes and transitioning to a circular green economy.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1^NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

Fast X-ray fluorescence microscopy provides high-throughput phenotyping of element distribution in seeds

The concentration, chemical speciation, and spatial distribution of essential and toxic mineral elements in cereal seeds have important implications for human health. To identify genes responsible for element uptake, translocation, and storage, high-throughput phenotyping methods are needed to visualize element distribution and concentration in seeds. Here, we used X-ray fluorescence microscopy (μ-XRF) as a method for rapid and high-throughput phenotyping of seed libraries and developed an ImageJ-based pipeline to analyze the spatial distribution of elements. Using this method, we nondestructively scanned 4,190 ethyl methanesulfonate (EMS)-mutagenized M1 rice (Oryza sativa) seeds and 533 diverse rice accessions in a genome-wide association study (GWAS) panel to simultaneously measure concentrations and spatial distribution of elements in the embryo, endosperm, and aleurone layer. A total of 692 putative mutants and 65 loci associated with the spatial distribution of elements in rice seed were identified. This powerful method provides a basis for investigating the genetics and molecular mechanisms controlling the accumulation and spatial variations of mineral elements in plant seeds.

Effects of Platinum Nanoparticles on Rice Seedlings (Oryza sativa L.): Size-dependent Accumulation, Transformation, and Ionomic Influence

Platinum nanoparticles (PtNPs) are increasing in the environment largely due to their wide use and application in automobile and medical industries. The mechanism of uptake behavior of different-sized PtNPs and their association with PtNPs-induced phytotoxicity to plants remains unclear. The present study investigated PtNP uptake mechanisms and phytotoxicity simultaneously to further understand the accumulation and transformation dynamics. The uptake mechanisms were investigated by comparing the uptake and toxicological effects of three different-sized PtNPs (25, 50, and 70 nm) on rice seedlings across an experimental concentration gradient (0.25, 0.5, and 1 mg/L) during germination. The quantitative and qualitative results indicated that 70 nm-sized PtNPs were more efficiently transferred in rice roots. The increase in the PtNP concentration restricted the particle uptake. Particle aggregation was common in plant cells and tended to dissolve on root surfaces. Notably, the dissolution of small particles was simultaneous with the growth of larger particles after PtNPs entered the rice tissues. Ionomic results revealed that PtNP accumulation induced element homeostasis in the shoot ionome. We observed a significant positive correlation between the PtNP concentration and Fe and B accumulation in rice shoots. Compared to particle size, the exposure concentration of PtNPs had a stronger effect on the shoot ionomic response. Our study provides better understanding of the correlation of ionomic change and NP quantitative accumulation induced by PtNPs in rice seedlings.

Mapping QTLs and gene validation studies for Mg2+ uptake and translocation using a MAGIC population in rice

Magnesium (Mg) is an essential element for plant growth and development. Rice is an important food crop in the world, but there are few studies on the uptake and translocation of Mg²⁺ in rice. We used a multi-parent advanced generation inter-cross (MAGIC) population constructed using four parental lines and genotyped by a 55 K rice SNP array for association analysis to locate QTLs related to Mg²⁺ uptake and translocation in rice at the seedling stage. Four QTLs (qRMg1, qRMg2, qRMg7 and qRMg8) were detected for the root Mg²⁺ concentration, which explained 11.45-13.08% of the phenotypic variation. The Mg²⁺ transporter gene, OsMGT1, was within the region of qRMg1. Three QTLs (qSMg3, qSMg7 and qSMg10) were detected for the shoot Mg²⁺ concentration, which explained 4.30-5.46% of the phenotypic variation. Two QTLs (qTrMg3 and qTrMg8) were found to affect the translocation of Mg²⁺ from the roots to the shoots, and explained 10.91% and 9.63% of phenotypic variation. qSMg3 and qTrMg3 might be the same, since they are very close to each other on chromosome 3. Analysis of candidate genes in the region of qSMg3 and qTrMg3 through qRT-PCR, complementation assay in the yeast Mg²⁺ transport-defective mutant CM66, and sequence analysis of the parental lines suggested that LOC_Os03g04360 may play important roles in Mg²⁺ uptake, translocation and accumulation in rice. Overexpression of LOC_Os03g04360 can significantly increase the Mg²⁺ concentration in rice seedlings, especially under the condition of low Mg²⁺ supply.

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.

Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages

Rice (Oryza sativa) is an important staple crop to address the Hidden Hunger problem not only in Asia but also in Africa where rice is fast becoming an important source of calories. The brown rice (whole grain with bran) is known to be more nutritious due to elevated mineral composition. The genetics underlying brown rice ionome (sum total of such mineral composition) remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies, gene set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms, was used. We identified 109 candidate genes with 5-20% phenotypic variation explained for the 12 micronutrients and identified epistatic interactions with multiple micronutrients. Pooling all candidate genes per micronutrient exhibited phenotypic variation explained values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles, which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through genome-wide association studies. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships and on the molecular mechanisms underlying micronutrient signatures.

Climate change challenges, plant science solutions

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.

Creation and gene expression analysis of a giant embryo rice mutant with high GABA content

Gamma-amino butyric acid (GABA) is a natural non-protein amino acid involved in stress, signal transmission, carbon and nitrogen balance, and other physiological processes in plants. In the human body, GABA has the effects of lowering blood pressure, anti-aging, and activating the liver and kidneys. However, there are few studies on the molecular regulation mechanism of genes in the metabolic pathways of GABA during grain development of giant embryo rice with high GABA content. In this study, three glant embryo (ge) mutants of different embryo sizes were obtained by CRISPR/Cas9 knockout, and it was found that GABA, protein, crude fat, and various mineral contents of the ge mutants were significantly increased. RNA-seq and qRT-PCR analysis showed that in the GABA shunt and polyamine degradation pathways, the expression levels of most of the genes encoding enzymes promoting GABA accumulation were significantly upregulated in the ge-1 mutant, whereas, the expression levels of most of the genes encoding enzymes involved GABA degradation were significantly downregulated in the ge-1 mutant. This is most likely responsible for the significant increase in GABA content of the ge mutant. These results help reveal the molecular regulatory network of GABA metabolism in giant embryo rice and provide a theoretical basis for the study of its development mechanisms, which is conducive to the rapid cultivation of GABA-rich rice varieties, promoting human nutrition, and ensuring health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01353-1.

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

Genome-wide association studies reveal genetic basis of ionomic variation in cassava

As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome-wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P-values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl-tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava.

CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.

Integration of multi-omics technologies for crop improvement: Status and prospects

With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.

A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid

Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F₂ s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.

Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective

Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia's most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.

Genome-Scale Profiling and High-Throughput Analyses Unravel the Genetic Basis of Arsenic Content Variation in Rice

Ionomics, the study of the composition of mineral nutrients and trace elements in organisms that represent the inorganic component of cells and tissues, has been widely studied to explore to unravel the molecular mechanism regulating the elemental composition of plants. However, the genetic factors of rice subspecies in the interaction between arsenic and functional ions have not yet been explained. Here, the correlation between As and eight essential ions in a rice core collection was analyzed, taking into account growing condition and genetic factors. The results demonstrated that the correlation between As and essential ions was affected by genetic factors and growing condition, but it was confirmed that the genetic factor was slightly larger with the heritability for arsenic content at 53%. In particular, the cluster coefficient of japonica (0.428) was larger than that of indica (0.414) in the co-expression network analysis for 23 arsenic genes, and it was confirmed that the distance between genes involved in As induction and detoxification of japonica was far than that of indica. These findings provide evidence that japonica populations could accumulate more As than indica populations. In addition, the cis-eQTLs of AIR2 (arsenic-induced RING finger protein) were isolated through transcriptome-wide association studies, and it was confirmed that AIR2 expression levels of indica were lower than those of japonica. This was consistent with the functional haplotype results for the genome sequence of AIR2, and finally, eight rice varieties with low AIR2 expression and arsenic content were selected. In addition, As-related QTLs were identified on chromosomes 5 and 6 under flooded and intermittently flooded conditions through genome-scale profiling. Taken together, these results might assist in developing markers and breeding plans to reduce toxic element content and breeding high-quality rice varieties in future.

Protecting plant nutrition from the effects of climate change

Climate change adversely affects plant nutrition, which serves as a major hurdle in the production of enough nutritious food to meet the needs of the growing global population. Here, we discuss how various climatic stressors impact nutrient homeostasis and how natural variation studies can yield resilient crop production systems to ensure future food security.

Genome-wide identification of PME gene family and expression of candidate genes associated with aluminum tolerance in tea plant (Camellia sinensis)

BACKGROUND

The major aluminum (Al) detoxication mechanism of tea plant (Camellia sinensis), as an Al hyperaccumulator plant, is the fixation of almost 70% of Al in the cell walls. Pectin is the primary constituent of cell walls, a degree of methylation of pectin polysaccharides regulated by the pectin methylesterase (PME) genes can greatly affect the Al binding capacity. The knowledge on PME gene family in tea plant is still poor.

RESULTS

We identified 66 (CsPME1-CsPME66) PME genes from C. sinensis genome. We studied their protein characterization, conserved motifs, gene structure, systematic evolution and gene expression under Al treatments, to establish a basis for in-depth research on the function of PMEs in tea plant. Gene structures analysis revealed that the majority of PME genes had 2-4 exons. Phylogenetic results pointed out that the PME genes from the same species displayed comparatively high sequence consistency and genetic similarity. Selective pressure investigation suggested that the Ka/Ks value for homologous genes of PME family was less than one. The expression of CsPMEs under three Al concentration treatments was tissue specific, eight PME genes in leaves and 15 in roots displayed a trend similar to of the Al contents and PME activities under Al concentration treatments, indicating that the degree of pectin de-esterification regulated by PME was crucial for Al tolerance of tea plant.

CONCLUSIONS

Sixty-six CsPME genes were identified for the first time in tea plant. The genome-wide identification, classification, evolutionary and transcription analyses of the PME gene family provided a new direction for further research on the function of PME gene in Al tolerance of tea plant.

Multi-Trait Genomic Prediction Models Enhance the Predictive Ability of Grain Trace Elements in Rice

Multi-trait (MT) genomic prediction models enable breeders to save phenotyping resources and increase the prediction accuracy of unobserved target traits by exploiting available information from non-target or auxiliary traits. Our study evaluated different MT models using 250 rice accessions from Asian countries genotyped and phenotyped for grain content of zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), and cadmium (Cd). The predictive performance of MT models compared to a traditional single trait (ST) model was assessed by 1) applying different cross-validation strategies (CV1, CV2, and CV3) inferring varied phenotyping patterns and budgets; 2) accounting for local epistatic effects along with the main additive effect in MT models; and 3) using a selective marker panel composed of trait-associated SNPs in MT models. MT models were not statistically significantly (p < 0.05) superior to ST model under CV1, where no phenotypic information was available for the accessions in the test set. After including phenotypes from auxiliary traits in both training and test sets (MT-CV2) or simply in the test set (MT-CV3), MT models significantly (p < 0.05) outperformed ST model for all the traits. The highest increases in the predictive ability of MT models relative to ST models were 11.1% (Mn), 11.5 (Cd), 33.3% (Fe), 95.2% (Cu) and 126% (Zn). Accounting for the local epistatic effects using a haplotype-based model further improved the predictive ability of MT models by 4.6% (Cu), 3.8% (Zn), and 3.5% (Cd) relative to MT models with only additive effects. The predictive ability of the haplotype-based model was not improved after optimizing the marker panel by only considering the markers associated with the traits. This study first assessed the local epistatic effects and marker optimization strategies in the MT genomic prediction framework and then illustrated the power of the MT model in predicting trace element traits in rice for the effective use of genetic resources to improve the nutritional quality of rice grain.

Sorghum Ionomics Reveals the Functional SbHMA3a Allele that Limits Excess Cadmium Accumulation in Grains

Understanding uptake and redistribution of essential minerals or sequestering of toxic elements is important for optimized crop production. Although the mechanisms controlling mineral transport have been elucidated in rice and other species, little is understood in sorghum-an important C4 cereal crop. Here, we assessed the genetic factors that govern grain ionome profiles in sorghum using recombinant inbred lines (RILs) derived from a cross between BTx623 and NOG (Takakibi). Pairwise correlation and clustering analysis of 22 elements, measured in sorghum grains harvested under greenhouse conditions, indicated that the parental lines, as well as the RILs, show different ionomes. In particular, BTx623 accumulated significantly higher levels of cadmium (Cd) than NOG, because of differential root-to-shoot translocation factors between the two lines. Quantitative trait locus (QTL) analysis revealed a prominent QTL for grain Cd concentration on chromosome 2. Detailed analysis identified SbHMA3a, encoding a P1B-type ATPase heavy metal transporter, as responsible for low Cd accumulation in grains; the NOG allele encoded a functional HMA3 transporter (SbHMA3a-NOG) whose Cd-transporting activity was confirmed by heterologous expression in yeast. BTx623 possessed a truncated, loss-of-function SbHMA3a allele. The functionality of SbHMA3a in NOG was confirmed by Cd concentrations of F2 grains derived from the reciprocal cross, in which the NOG allele behaved in a dominant manner. We concluded that SbHMA3a-NOG is a Cd transporter that sequesters excess Cd in root tissues, as shown in other HMA3s. Our findings will facilitate the isolation of breeding cultivars with low Cd in grains or in exploiting high-Cd cultivars for phytoremediation.

Relationships Among Arsenic-Related Traits, Including Rice Grain Arsenic Concentration and Straighthead Resistance, as Revealed by Genome-Wide Association

There is global concern that rice grains and foods can contain harmful amounts of arsenic (As), motivating breeders to produce cultivars that restrict As accumulation in grains to protect human health. Arsenic is also toxic to plants, with straighthead disorder (StHD), causing panicle sterility, being observed in rice. The genetic variation in StHD resistance suggests that plants have evolved mechanisms that reduce As toxicity, possibly via regulation of As uptake, transport, or detoxification/sequestration. Because these mechanisms could also underlie the wide (3- to 100-fold) differences in grain As concentration (grain-As) observed among diverse rice genotypes, it was hypothesized that some genes reduce both grain-As content and StHD susceptibility and may be detectable as co-located StDH and As quantitative trait loci (QTL). We used a machine-learning Bayesian network approach plus high-resolution genome-wide association study (GWAS) to identify QTL for grain-As and StHD resistance within the USDA Rice Minicore Collection (RMC). Arsenic enters roots through phosphorus (P) and silica (Si) transporters, As detoxification involves sulfur (S), and cell signaling to activate stress tolerance mechanisms is impacted by Si, calcium (Ca), and copper (Cu). Therefore, concentrations of Si, P, S, Ca, and Cu were included in this study to elucidate physiological mechanisms underlying grain-As and StHD QTL. Multiple QTL (from 9 to 33) were identified for each of the investigated As-associated traits. Although the QTL for StHD, Si, and grain-As did not overlap as heavily as our hypothesis predicted (4/33 StHD and 4/15 As QTL co-located), they do provide useful guidance to future research. Furthermore, these are the first StHD and Si QTL to be identified using high-density mapping, resulting in their being mapped to shorter, more precise genomic regions than previously reported QTL. The candidate genes identified provide guidance for future research, such as gene editing or mutation studies to further investigate the role of antioxidants and ROS scavenging to StHD resistance, as indicated by candidate genes around the commonly reported qStHD8-2 QTL. Other genes indicated for future study for improving grain-As and StHD include several multidrug and toxic compound extrusion (MATE) genes, F-box genes, and NIPs not documented to date to transport As.

The rice heavy-metal transporter OsNRAMP1 regulates disease resistance by modulating ROS homoeostasis

Crop diseases threaten food security and sustainable agriculture. Consumption of crops containing nonessential toxic metals leads to health risks for humans. Therefore, cultivation of disease-resistant and toxic metal-safe crops is a double-gain strategy that can contribute to food security. Here, we show that rice heavy-metal transporter OsNRAMP1 plays an important role in plant immunity by modulating metal ion and reactive oxygen species (ROS) homoeostasis. OsNRAMP1 expression was induced after pathogenic bacteria and fungi infections. The osnramp1 mutants had an increased content of H₂ O₂ and activity of superoxide dismutase, but decreased activity of catalase, showing enhanced broad-spectrum resistance against bacterial and fungal pathogens. RNA-seq analysis identified a number of differentially expressed genes that were involved in metal ion and ROS homoeostasis. Altered expression of metal ion-dependent ROS-scavenging enzymes genes and lower accumulation of cations such as Mn together induced compromised metal ion-dependent enzyme-catalysing activity and modulated ROS homoeostasis, which together contributed towards disease resistance in osnramp1 mutants. Furthermore, the osnramp1 mutants contained lower levels of toxic heavy metals Cd and Pb and micronutrients Ni and Mn in leaves and grains. Taken together, a proof of concept was achieved that broad-spectrum disease-resistant and toxic heavy-metal-safe rice was engineered by removal of the OsNRAMP1 gene.

Molybdenum: More than an essential element

Molybdenum (Mo) is an essential element for almost all living organisms. After being taken up into the cells as molybdate, it is incorporated into the molybdenum cofactor, which functions as the active site of several molybdenum-requiring enzymes and thus plays crucial roles in multiple biological processes. The uptake and transport of molybdate is mainly mediated by two types of molybdate transporters. The homeostasis of Mo in plant cells is tightly controlled, and such homeostasis likely plays vital roles in plant adaptation to local environments. Recent evidence suggests that Mo is more than an essential element required for plant growth and development; it is also involved in local adaptation to coastal salinity. In this review, we summarize recent research progress on molybdate uptake and transport, molybdenum homeostasis network in plants, and discuss the potential roles of the molybdate transporter in plant adaptation to their local environment.

Micronutrient homeostasis in plants for more sustainable agriculture and healthier human nutrition

The provision of sustainable, sufficient, and nutritious food to the growing population is a major challenge for agriculture and the plant research community. In this respect, the mineral micronutrient content of food crops deserves particular attention. Micronutrient deficiencies in cultivated soils and plants are a global problem that adversely affects crop production and plant nutritional value, as well as human health and well-being. In this review, we call for awareness of the importance and relevance of micronutrients in crop production and quality. We stress the need for better micronutrient nutrition in human populations, not only in developing but also in developed nations, and describe strategies to identify and characterize new varieties with high micronutrient content. Furthermore, we explain how adequate nutrition of plants with micronutrients impacts metabolic functions and the capacity of plants to express tolerance mechanisms against abiotic and biotic constraints. Finally, we provide a brief overview and a critical discussion on current knowledge, future challenges, and specific technological needs for research on plant micronutrient homeostasis. Research in this area is expected to foster the sustainable development of nutritious and healthy food crops for human consumption.

The Vacuolar Molybdate Transporter OsMOT1;2 Controls Molybdenum Remobilization in Rice

Molybdenum (Mo) is an essential micronutrient for almost all living organisms. The Mo uptake process in plants has been well investigated. However, the mechanisms controlling Mo translocation and remobilization among different plant tissues are largely unknown, especially the allocation of Mo to rice grains that are the major dietary source of Mo for humans. In this study, we characterized the functions of a molybdate transporter, OsMOT1;2, in the interorgan allocation of Mo in rice. Heterologous expression in yeast established the molybdate transport activity of OsMOT1;2. OsMOT1;2 was highly expressed in the blades of the flag leaf and the second leaf during the grain filling stage. Subcellular localization revealed that OsMOT1;2 localizes to the tonoplast. Knockout of OsMOT1;2 led to more Mo accumulation in roots and less Mo translocation to shoots at the seedling stage and to grains at the maturity stage. The remobilization of Mo from older leaves to young leaves under molybdate-depleted condition was also decreased in the osmot1;2 knockout mutant. In contrast, overexpression of OsMOT1;2 enhanced the translocation of Mo from roots to shoots at the seedling stage. The remobilization of Mo from upper leaves to grains was also enhanced in the overexpression lines during grain filling. Our results suggest that OsMOT1;2 may function as a vacuolar molybdate exporter facilitating the efflux of Mo from the vacuole into the cytoplasm, and thus, it plays an important role in the root-to-shoot translocation of Mo and the remobilization of Mo from leaves to grains.

Genome-Wide Association Study Reveals Genomic Regions Associated With Molybdenum Accumulation in Wheat Grains

Molybdenum (Mo) is an essential micronutrient for almost all organisms. Wheat, a major staple crop worldwide, is one of the main dietary sources of Mo. However, the genetic basis for the variation of Mo content in wheat grains remains largely unknown. Here, a genome-wide association study (GWAS) was performed on the Mo concentration in the grains of 207 wheat accessions to dissect the genetic basis of Mo accumulation in wheat grains. As a result, 77 SNPs were found to be significantly associated with Mo concentration in wheat grains, among which 52 were detected in at least two sets of data and distributed on chromosome 2A, 7B, and 7D. Moreover, 48 out of the 52 common SNPs were distributed in the 726,761,412-728,132,521 bp genomic region of chromosome 2A. Three putative candidate genes, including molybdate transporter 1;2 (TraesCS2A02G496200), molybdate transporter 1;1 (TraesCS2A02G496700), and molybdopterin biosynthesis protein CNX1 (TraesCS2A02G497200), were identified in this region. These findings provide new insights into the genetic basis for Mo accumulation in wheat grains and important information for further functional characterization and breeding to improve wheat grain quality.

Genome-Wide Association Analysis Reveals Genetic Loci and Candidate Genes for Chest, Abdominal, and Waist Circumferences in Two Duroc Pig Populations

Chest circumference (CC), abdominal circumference (AC), and waist circumference (WC) are regarded as important indicators for improving economic traits because they can reflect the growth and physiological status in pigs. However, the genetic architecture of CC, AC, and WC is still elusive. Here, we performed single-trait and multi-trait genome-wide association studies (GWASs) for CC, AC, and WC in 2,206 American origin Duroc (AOD) and 2,082 Canadian origin Duroc (COD) pigs. As a result, one novel quantitative trait locus (QTL) on Sus scrofa chromosome (SSC) one was associated with CC and AC in COD pigs, which spans 6.92 Mb (from 170.06 to 176.98 Mb). Moreover, multi-trait GWAS identified 21 significant SNPs associated with the three conformation traits, indicating the multi-trait GWAS is a powerful statistical approach that uncovers pleiotropic locus. Finally, the three candidate genes (ITGA11, TLE3, and GALC) were selected that may play a role in the conformation traits. Further bioinformatics analysis indicated that the candidate genes for the three conformation traits mainly participated in sphingolipid metabolism and lysosome pathways. For all we know, this study was the first GWAS for WC in pigs. In general, our findings further reveal the genetic architecture of CC, AC, and WC, which may offer a useful reference for improving the conformation traits in pigs.

Microbiome-wide association studies between phyllosphere microbiota and ionome highlight the beneficial symbiosis of Lactococcus lactis in alleviating aluminium in cassava

The phyllosphere is one of the most abundant habitats for global microbiota. The ionome is the composition of mineral elements in plants. The correlation between phyllosphere microbiota and the ionome remains elusive in plants, especially in the most important tropical crop cassava. In this study, microbiome-wide association studies (MWASs) of thirty varieties were performed to reveal the association between phyllosphere microbiota and ionomic variations in cassava. Annotation of metagenomic species identified some species that were significantly correlated with ionomic variations in cassava. Among them, Lactococcus lactis abundance was negatively associated with leaf aluminium (Al) levels but positively related to leaf potassium (K) levels. Notably, both the reference and isolated L. lactis showed strong binding capacity to Al. Further bacterial transplantation of isolated L. lactis could significantly decrease endogenous Al levels but increase K levels in cassava, and it can also lead to increased citric acid and lactic acid levels as well as higher transcript levels of K uptake-related genes. Taken together, this study reveals the involvement of phyllosphere microbiota in ionomic variation in cassava, and the correlation between L. lactis abundance and Al and K levels provides novel insights into alleviating Al accumulation and promoting K uptake simultaneously.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

Toxic metals and metalloids: Uptake, transport, detoxification, phytoremediation, and crop improvement for safer food

Agricultural soils are under threat of toxic metal/metalloid contamination from anthropogenic activities, leading to excessive accumulation of arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) in food crops that poses significant risks to human health. Understanding how these toxic metals and their methylated species are taken up, translocated, and detoxified is prerequisite to developing strategies to limit their accumulation for safer food. Toxic metals are taken up and transported across different cellular compartments and plant tissues via various transporters for essential or beneficial nutrients, e.g. As by phosphate and silicon transporters, and Cd by manganese (Mn), zinc (Zn), and iron (Fe) transporters. These transport processes are subjected to interactions with nutrients and the regulation at the transcriptional and post-translational levels. Complexation with thiol-rich compounds, such as phytochelatins, and sequestration in the vacuoles are the common mechanisms for detoxification and for limiting their translocation. A number of genes involved in toxic metal uptake, transport, and detoxification have been identified, offering targets for genetic manipulation via gene editing or transgenic technologies. Natural variations in toxic metal accumulation exist within crop germplasm, and some of the quantitative trait loci underlying these variations have been cloned, paving the way for marker-assisted breeding of low metal accumulation crops. Using plants to extract and remove toxic metals from soil is also possible, but this phytoremediation approach requires metal hyperaccumulation for efficiency. Knowledge gaps and future research needs are also discussed.

Zinc in plants: Integrating homeostasis and biofortification

Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn²⁺ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.

From Green Super Rice to green agriculture: Reaping the promise of functional genomics research

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.