Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq

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.

In-situ remediation of cadmium contamination in paddy fields: from rhizosphere soil to rice kernel

Cadmium (Cd) has become an important heavy metal pollutant because of its strong migration and high toxicity. The industrial production process aggravated the Cd pollution in rice fields. Human exposure to Cd through rice can cause kidney damage, emphysema, and various cardiovascular and metabolic diseases, posing a grave threat to health. As modern technology develops, the Cd accumulation model in rice and in-situ remediation of Cd pollution in cornfields have been extensively studied and applied, so it is necessary to sort out and summarize them systematically. Therefore, this paper reviewed the primary in-situ methods for addressing heavy metal contamination in rice paddies, including chemical remediation (inorganic-organic fertilizer remediation, nanomaterials, and composite remediation), biological remediation (phytoremediation and microbial remediation), and crop management remediation technologies. The factors that affect Cd transformation in soil and Cd migration in crops, the advantages and disadvantages of remediation techniques, remediation mechanisms, and the long-term stability of remediation were discussed. The shortcomings and future research directions of in situ remediation strategies for heavily polluted paddy fields and genetic improvement strategies for low-cadmium rice varieties were critically proposed. To sum up, this review aims to enhance understanding and serve as a reference for the appropriate selection and advancement of remediation technologies for rice fields contaminated with heavy metals.

Genetic mapping of regions associated with root system architecture in rice using MutMap QTL-seq

The root system architecture is an important complex trait in rice. With changing climatic conditions and soil nutrient deficiencies, there is an immediate need to breed nutrient-use-efficient rice varieties with robust root system architectural (RSA) traits. To map the genomic regions associated with crucial component traits of RSA viz. root length and root volume, a biparental F2 mapping population was developed using TI-128, an Ethyl Methane Sulphonate (EMS) mutant of a mega variety BPT-5204 having high root length (RL) and root volume (RV) with wild type BPT-5204. Extreme bulks having high RL and RV and low RL and RV were the whole genome re-sequenced along with parents. Genetic mapping using the MutMap QTL-Seq approach elucidated two genomic intervals on Chr.12 (3.14-3.74 Mb, 18.11-20.85 Mb), and on Chr.2 (23.18-23.68 Mb) as potential regions associated with both RL and RV. The Kompetitive Allele Specific PCR (KASP) assays for SNPs with delta SNP index near 1 were associated with higher RL and RV in the panel of sixty-two genotypes varying in root length and volume. The KASP_SNPs viz. Chr12_S4 (C→T; Chr12:3243938), located in the 3' UTR region of LOC_Os12g06670 encoding a protein kinase domain-containing protein and Chr2_S6 (C→T; Chr2:23181622) present upstream in the regulator of chromosomal condensation protein LOC_Os2g38350. Validation of these genes using qRT-PCR and in-silico studies using various online tools and databases revealed higher expression in TI-128 as compared to BPT- 5204 at the seedling and panicle initiation stages implying the functional role in enhancing RL and RV.

Transcriptome sequencing analysis of gene expression in phosphate-solubilizing bacterium 'N3' and grafted watermelon plants coping with toxicity induced by cadmium

Cadmium (Cd) is a harmful metal in soil, and reducing Cd accumulation in plants has become a vital prerequisite for maintaining food safety. Phosphate-solubilizing bacteria (PSB) can not only improve plant growth but also inhibit the transportation of metals to roots. However, data on gene expression in PSB Burkholderia sp. strain 'N3' and grafted watermelon plants dealing with Cd remain to be elucidated. In this study, core genes and metabolic pathways of strain 'N3' and grafted plants were analyzed by Illumina sequencing. Results showed that 356 and 2527 genes were upregulated in 'N3' and grafted watermelon plants, respectively, whereas 514 and 1540 genes were downregulated in 'N3' and grafted watermelon plants, respectively. Gene ontology enrichment analysis showed that signal transduction, inorganic ion transport, cell motility, amino acid transport, and metabolism pathways were marked in 'N3'. However, pathways such as secondary metabolite biosynthesis, oxidation-reduction process, electron transfer activity, and channel regulator activity were marked in the grafted plants. Six genes related to pentose phosphate, glycolysis, and gluconeogenesis metabolism were upregulated in the grafted plants. This study paves the way for developing potential strategies to improve plant growth under Cd toxicity.

MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization

BACKGROUND

Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest.

RESULTS

We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature.

CONCLUSIONS

MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available.

AVAILABILITY AND IMPLEMENTATION

MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools .

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

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

Ectopic expression of SaCTP3 from the hyperaccumulator Sedum alfredii in sorghum increases Cd accumulation for phytoextraction

The Cd tolerance protein SaCTP3, which responds to Cd stress, was identified in Sedum alfredii; however, how to improve the efficiency of phytoremediation of Cd-contaminated soil using the CTP gene remains unknown. In this study, the phytoremediation potential of SaCTP3 of Sedum alfredii was identified. In the yeast Cd-sensitive strain Δycf1 overexpressing SaCTP3, the accumulation of Cd was higher than that in the Δycf1 strain overexpressing an empty vector. Transgenic sorghum plants overexpression SaCTP3 were further constructed to verify the function of SaCTP3. Compared to wild-type plants, the SaCTP3-overexpressing lines exhibited higher Cd accumulation under 500 μM Cd conditions. The average Cd content inSaCTP3-overexpressing plants is more than four times higher than that of WT plants. This was accompanied by an enhanced ability to scavenge ROS, as evidenced by the significantly increased activities of peroxidase, catalase, and superoxide dismutase in response to Cd stress. Pot experiments further demonstrated that SaCTP3 overexpression resulted in improved soil Cd scavenging and photosynthetic abilities. After 20 days of growth, the average Cd content in the soil planted with SaCTP3-overexpressing sorghum decreased by 19.4%, while the residual Cd content in the soil planted with wild-type plants was only reduced by 5.4%. This study elucidated the role of SaCTP3 from S.alfredii, highlighting its potential utility in genetically modifying sorghum for the effective phytoremediation of Cd.

Mutation of OsNRAMP5 reduces cadmium xylem and phloem transport in rice plants and its physiological mechanism

Natural resistance associated macrophage protein 5 (NRAMP5) is a key transporter for cadmium (Cd) uptake by rice roots; however, the effect of OsNRAMP5 on Cd translocation and redistribution in rice plants remains unknown. In this study, an extremely low Cd-accumulation mutant (lcd1) and wild type (WT) plants were utilized to investigate the effect of OsNRAMP5 mutation on Cd translocation and redistribution via the xylem and phloem and its possible physiological mechanism using field, hydroponic and isotope-labelling experiments. The results showed that OsNRAMP5 mutation reduced xylem and phloem transport of Cd, due to remarkably lower Cd translocation from roots to shoots and from the leaves Ⅰ-Ⅲ to their corresponding nodes, as well as lower Cd concentrations in xylem and phloem sap of lcd1 compared to WT plants. Mutation of OsNRAMP5 reduced Cd translocation from roots to shoots in lcd1 plants by increasing Cd deposition in cellulose of root cell walls and reducing OsHMA2-and OsCCX2-mediated xylem loading of Cd, and the citric acid- and tartaric acid-mediated long-distance xylem transport of Cd. Moreover, OsNRAMP5 mutation inhibited Cd redistribution from flag leaves to nodes and panicles in lcd1 plants by increasing Cd sequestration in cellulose and vacuoles, and decreasing OsLCT1-mediated Cd phloem transport in flag leaves.

Mapping and Screening of Candidate Gene Regulating the Biomass Yield of Sorghum (Sorghum bicolor L.)

Biomass yield is one of the important traits of sorghum, which is greatly affected by leaf morphology. In this study, a lobed-leaf mutant (sblob) was screened and identified, and its F2 inbred segregating line was constructed. Subsequently, MutMap and whole-genome sequencing were employed to identify the candidate gene (sblob1), the locus of which is Sobic.003G010300. Pfam and homologous analysis indicated that sblob1 encodes a Cytochrome P450 protein and plays a crucial role in the plant serotonin/melatonin biosynthesis pathway. Structural and functional changes in the sblob1 protein were elucidated. Hormone measurements revealed that sblob1 regulates both leaf morphology and sorghum biomass through regulation of the melatonin metabolic pathway. These findings provide valuable insights for further research and the enhancement of breeding programs, emphasizing the potential to optimize biomass yield in sorghum cultivation.

Molecular-Assisted Breeding of Cadmium Pollution-Safe Cultivars

Cadmium (Cd) contamination in edible agricultural products, especially in crops intended for consumption, has raised worldwide concerns regarding food safety. Breeding of Cd pollution-safe cultivars (Cd-PSCs) is an effective solution to preventing the entry of Cd into the food chain from contaminated agricultural soil. Molecular-assisted breeding methods, based on molecular mechanisms for cultivar-dependent Cd accumulation and bioinformatic tools, have been developed to accelerate and facilitate the breeding of Cd-PSCs. This review summarizes the recent progress in the research of the low Cd accumulation traits of Cd-PSCs in different crops. Furthermore, the application of molecular-assisted breeding methods, including transgenic approaches, genome editing, marker-assisted selection, whole genome-wide association analysis, and transcriptome, has been highlighted to outline the breeding of Cd-PSCs by identifying critical genes and molecular biomarkers. This review provides a comprehensive overview of the development of Cd-PSCs and the potential future for breeding Cd-PSC using modern molecular technologies.

Multiple insights into lignin-mediated cadmium detoxification in rice (Oryza sativa)

Cadmium (Cd) is readily absorbed by rice and enters the food chain, posing a health risk to humans. A better understanding of the mechanisms of Cd-induced responses in rice will help in developing solutions to reduce Cd uptake in rice. Therefore, this research attempted to reveal the detoxification mechanisms of rice in response to Cd through physiological, transcriptomic and molecular approaches. The results showed that Cd stress restricted rice growth, led to Cd accumulation and H2O2 production, and resulted cell death. Transcriptomic sequencing revealed glutathione and phenylpropanoid were the major metabolic pathways under Cd stress. Physiological studies showed that antioxidant enzyme activities, glutathione and lignin contents were significantly increased under Cd stress. In response to Cd stress, q-PCR results showed that genes related to lignin and glutathione biosynthesis were upregulated, whereas metal transporter genes were downregulated. Further pot experiment with rice cultivars with increased and decreased lignin content confirmed the causal relationship between increased lignin and reduced Cd in rice. This study provides a comprehensive understanding of lignin-mediated detoxification mechanism in rice under Cd stress and explains the function of lignin in production of low-Cd rice to ensure human health and food safety.

Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice

Complete panicle exsertion (CPE) in rice is an important determinant of yield and a desirable trait in breeding. However, the genetic basis of CPE in rice still remains to be completely characterized. An ethyl methane sulfonate (EMS) mutant line of an elite cultivar Samba Mahsuri (BPT 5204), displaying stable and consistent CPE, was identified and named as CPE-110. MutMap and RNA-seq were deployed for unraveling the genomic regions, genes, and markers associated with CPE. Two major genomic intervals, on chromosome 8 (25668481-25750456) and on chromosome 11 (20147154-20190400), were identified to be linked to CPE through MutMap. A non-synonymous SNP (G/A; Chr8:25683828) in the gene LOC_Os08g40570 encoding pyridoxamine 5'-phosphate oxidase with the SNP index 1 was converted to Kompetitive allele-specific PCR (KASP) marker. This SNP (KASP 8-1) exhibited significant association with CPE and further validated through assay in the F2 mapping population, released varieties and CPE exhibiting BPT 5204 mutant lines. RNA-seq of the flag leaves at the booting stage, 1100 genes were upregulated and 1305 downregulated differentially in CPE-110 and BPT 5204. Metabolic pathway analysis indicated an enrichment of genes involved in photosynthesis, glyoxylate, dicarboxylate, porphyrin, pyruvate, chlorophyll, carotenoid, and carbon metabolism. Further molecular and functional studies of the candidate genes could reveal the mechanistic aspects of CPE.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01412-1.

Nodes play a major role in cadmium (Cd) storage and redistribution in low-Cd-accumulating rice (Oryza sativa L.) cultivars

Rice cadmium (Cd) contamination is one of the critical agricultural issues. Breeding of low-Cd-accumulating cultivar is an effective approach to reduce Cd bioaccumulation in rice. To investigate the molecular mechanism underlying Cd transport in rice, the functions of nodes in Cd transport are explored. The results show that different nodes have different functions of Cd transport in the rice plant and the physiological structure of the first node under panicle (N1) determine the Cd accumulation in the brown rice. The upper nodes can redistribute the Cd transport in aboveground tissues. The expressions of Cd-efflux transporter genes (OsLCT1 and OsHMA2) located on the plasma-membrane are the main factors affecting the Cd transport form node to brown rice, which are more depended on the node functions but not the node Cd concentrations. Lower expressions of OsLCT1 and OsHMA2 in N1 result in lower Cd transport from node to brown rice. The size of vascular-bundle (VB) areas in the junctional node with the flag leaf can determine the expression of OsHMA2 and the expression of OsLCT1 positively correlated with the Cd transport ability of first node (N1). The expressions of OsVIT2 and OsABCC1 cannot allow Cd to be immobilized into the vacuoles in node. The VB structure and Cd transporter gene expression level of N1 proved that the Cd concentration of N1 can be used as an important indicator for screening low-Cd-accumulating cultivars. The major implication is that selecting or breeding cultivars with lower Cd accumulations in N1 could be an effective strategy to reduce Cd accumulation in rice grains.

Comparative Transcriptome Analysis Reveals Complex Physiological Response and Gene Regulation in Peanut Roots and Leaves under Manganese Toxicity Stress

Excess Manganese (Mn) is toxic to plants and reduces crop production. Although physiological and molecular pathways may drive plant responses to Mn toxicity, few studies have evaluated Mn tolerance capacity in roots and leaves. As a result, the processes behind Mn tolerance in various plant tissue or organ are unclear. The reactivity of peanut (Arachis hypogaea) to Mn toxicity stress was examined in this study. Mn oxidation spots developed on peanut leaves, and the root growth was inhibited under Mn toxicity stress. The physiological results revealed that under Mn toxicity stress, the activities of antioxidases and the content of proline in roots and leaves were greatly elevated, whereas the content of soluble protein decreased. In addition, manganese and iron ion content in roots and leaves increased significantly, but magnesium ion content decreased drastically. The differentially expressed genes (DEGs) in peanut roots and leaves in response to Mn toxicity were subsequently identified using genome-wide transcriptome analysis. Transcriptomic profiling results showed that 731 and 4589 DEGs were discovered individually in roots and leaves, respectively. Furthermore, only 310 DEGs were frequently adjusted and controlled in peanut roots and leaves, indicating peanut roots and leaves exhibited various toxicity responses to Mn. The results of qRT-PCR suggested that the gene expression of many DEGs in roots and leaves was inconsistent, indicating a more complex regulation of DEGs. Therefore, different regulatory mechanisms are present in peanut roots and leaves in response to Mn toxicity stress. The findings of this study can serve as a starting point for further research into the molecular mechanism of important functional genes in peanut roots and leaves that regulate peanut tolerance to Mn poisoning.

The mechanism of enhanced lignin regulating foliar Cd absorption and yield in rice (Oryza sativa L.)

The impact of atmospheric deposition of cadmium (Cd) in cereal crops has become a global concern. Enhanced lignin content was expected to benefit the plant performance against Cd exposure. To date, however, the underlying mechanisms of lignin regulating foliar Cd absorption in rice (Oryza sativa L.) and its effect on grain yield remains unclear. In present study, the effect and mechanism of rice in response to leaf Cd exposure were investigated using 113Cd stable isotope and a lignin-increased rice mutant. The highest Cd uptake efficiency and uptake amount was observed in wild type (WT) plant grown in the maturity period, which were 3-fold higher than in mutant plant. Compared to WT, the mutant exhibited 14.75% and 25.43% higher contents in G- and S-unit of lignin monomers. Lignin biosynthesis and polymerization related genes (OsPAL/OsCOMT/Os4CL3/OsLAC5/OsLAC15) were significantly up-regulated in mutants. In addition, the enzyme activities involved in the above process were also significantly increased by 1.24-1.49-fold. The increased Cd retention in cell wall and decreased gene expression levels of OsNRAMP5, OsHMA3 and OsIRT1 in mutant indicated that lignin effectively inhibited Cd transportion in plant tissues. Moreover, the antioxidant capacity and photosynthesis efficiency in mutant plant were obviously improved, leading to higher Cd tolerance and increased grain yield. Our results revealed the molecular and physiological mechanisms of enhanced lignin regulating foliar Cd absorption and yield in rice, and provided the valuable rice genotype to ensure food safety.

Knockout of OsNRAMP5 enhances rice tolerance to cadmium toxicity in response to varying external cadmium concentrations via distinct mechanisms

OsNRAMP5 is a transporter responsible for cadmium (Cd) and manganese (Mn) uptake and root-to-shoot translocation of Mn in rice plants. Knockout of OsNRAMP5 is regarded as an effective approach to minimize Cd uptake and accumulation in rice. It is vital to evaluate the effects of knocking out OsNRAMP5 on Cd and Mn accumulation, as well as Cd tolerance of rice plants in response to varying environmental Cd concentrations, and to uncover the underlying mechanism, which until now, has remained largely unexplored. This study showed that knockout of OsNRAMP5 decreased Cd uptake, but simultaneously facilitated Cd translocation from roots to shoots. The effect of OsNRAMP5 knockout on reducing root Cd uptake weakened, however its effect on improving root-to-shoot Cd translocation was constant with increasing environmental Cd concentrations. As a result, its mutation dramatically reduced Cd accumulation in shoots under low and moderate Cd stress, but inversely increased that under high Cd conditions. Interestingly, Cd tolerance of its knockout mutants was persistently enhanced, irrespective of lower or higher Cd concentrations in shoots, compared with that of wild-type plants. Knockout of OsNRAMP5 mitigated Cd toxicity by dramatically diminishing Cd uptake at low or moderate external Cd concentrations. Remarkably, its knockout effectively complemented deficient mineral nutrients in shoots, thereby indirectly enhancing rice tolerance to severe Cd stress. Additionally, its mutation conferred preferential delivery of Mn to young leaves and grains. These results have important implications for the application of the OsNRAMP5 mutation in mitigating Cd toxicity and lowering the risk of excessive Cd accumulation in rice grains.

Alkaline Stress Induces Different Physiological, Hormonal and Gene Expression Responses in Diploid and Autotetraploid Rice

Saline−alkaline stress is a critical abiotic stress that negatively affects plants’ growth and development. Considerably higher enhancements in plant tolerance to saline−alkaline stress have often been observed in polyploid plants compared to their diploid relatives, the underlying mechanism of which remains elusive. In this study, we explored the variations in morphological and physiological characteristics, phytohormones, and genome-wide gene expression between an autotetraploid rice and its diploid relative in response to alkaline stress. It was observed that the polyploidization in the autotetraploid rice imparted a higher level of alkaline tolerance than in its diploid relative. An eclectic array of physiological parameters commonly used for abiotic stress, such as proline, soluble sugars, and malondialdehyde, together with the activities of some selected antioxidant enzymes, was analyzed at five time points in the first 24 h following the alkaline stress treatment between the diploid and autotetraploid rice. Phytohormones, such as abscisic acid and indole-3-acetic acid were also comparatively evaluated between the two types of rice with different ploidy levels under alkaline stress. Transcriptomic analysis revealed that gene expression patterns were altered in accordance with the variations in the cellular levels of phytohormones between diploid and autotetraploid plants upon alkaline stress. In particular, the expression of genes related to peroxide and transcription factors was substantially upregulated in autotetraploid plants compared to diploid plants in response to the alkaline stress treatment. In essence, diploid and autotetraploid rice plants exhibited differential gene expression patterns in response to the alkaline stress, which may shed more light on the mechanism underpinning the ameliorated plant tolerance to alkaline stress following genome duplication.

Mapping and functional analysis of high-copper accumulation mutant oshc1 in rice

Copper (Cu) is an essential but potentially toxic element in rice. Little is known about the mechanism of rice grain Cu accumulation. In this study, we identified a high copper accumulation in grain 1 (oshc1) mutant from the wild type indica rice cultivar 9311 (WT) mutant bank. Compared with those in WT, more Cu was shown to accumulate in the shoots of seedlings and the above-ground tissues except nodes although less total Cu content in oshc1. Further analysis showed that the mutant had an accelerated Cu transport ratio from roots to shoots and higher Cu concentration in xylem sap than WT. This phenomenon in oshc1 was controlled by a single recessive gene, which was identified as BGIOSGA007732, and named OsHMA4. The eight base frame-shift from 1021 to 1028 bp in the coding sequence of OsHMA4 led to a modification after the 341st amino acid and resulted in premature translation termination of OsHMA4 at the 377th amino acid. This may change the function of OsHMA4. Furthermore, the up-regulated OsCOPT7 and OsATX1 and down-regulated OsHMA4 probably decrease Cu compartmentalization in roots of oshc1. In summary, the frame-shift in OsHMA4 changes the function of OsHMA4 and the expression of genes relative to Cu transport in the mutant, which leads to more Cu transport upward and higher Cu accumulation in the rice grains. Moreover, oshc1 was more tolerance to Cu-shortage than WT, while more sensitive to Cu excess exposure than WT. However, RNA-Seq analysis shown that changes in transcription levels of genes in oshc1 involving in molecular function of ions binding and biological processes of cell wall organization and defense response to bio-stress. Which indicates that oshc1 is advantage to Cu limited condition than WT. This work reveals the mechanism of high Cu accumulation in the grains of oshc1 and provides a material to breed new cultivars with optimum levels of Cu in brown rice by crossing with other dominant varieties, which can be planted in different soils to ensure the yield and quality of rice.

Bulk segregation analysis in the NGS era: a review of its teenage years

Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.

Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes

Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.

Stress signaling convergence and nutrient crosstalk determine zinc-mediated amelioration against cadmium toxicity in rice

Consumption of rice (Oryza sativa L.) is one of the major pathways for heavy metal bioaccumulation in humans over time. Understanding the molecular responses of rice to heavy metal contamination in agriculture is useful for eco-toxicological assessment of cadmium (Cd) and its interaction with zinc (Zn). In certain crops, the impacts of Cd stress or Zn nutrition on the biophysical chemistry and gene expression have been widely investigated, but their molecular interactions at transcriptomic level, particularly in rice roots, are still elusive. Here, hydroponic investigations were carried out with two rice genotypes (Yinni-801 and Heizhan-43), varying in Cd contents in plant tissues to determine their transcriptomic responses upon Cd15 (15 µM) and Cd15+Zn50 (50 µM) treatments. High throughput RNA-sequencing analysis confirmed that 496 and 2407 DEGs were significantly affected by Cd15 and Cd15+Zn50, respectively, among which 1016 DEGs were commonly induced in both genotypes. Multitude of DEGs fell under the category of protein kinases, such as calmodulin (CaM) and calcineurin B-like protein-interacting protein kinases (CBL), indicating a dynamic shift in hormonal signal transduction and Ca2+ involvement with the onset of treatments. Both genotypes expressed a mutual regulation of transcription factors (TFs) such as WRKY, MYB, NAM, AP2, bHLH and ZFP families under both treatments, whereas genes econding ABC transporters (ABCs), high affinity K+ transporters (HAKs) and Glutathione-S-transferases (GSTs), were highly up-regulated under Cd15+Zn50 in both genotypes. Zinc addition triggered more signaling cascades and detoxification related genes in regulation of immunity along with the suppression of Cd-induced DEGs and restriction of Cd uptake. Conclusively, the effective integration of breeding techniques with candidate genes identified in this study as well as economically and technologically viable methods, such as Zn nutrient management, could pave the way for selecting cultivars with promising agronomic qualities and reduced Cd for sustainable rice production.

Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress

It is known that organisms have developed various mechanisms to cope with cadmium (Cd) stress, while we still lack a system-level understanding of the functional isomorphy among them. In the present study, a cross-kingdom comparison was conducted among Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii, through toxicological tests, comparative transcriptomics, as well as conventional functional genomics. An equivalent level of Cd stress was determined via inhibition tests. Through transcriptome comparison, the three organisms exhibited differential gene expression under the same Cd stress relative to the corresponding no-treatment control. Results from functional enrichment analysis of differentially expressed genes (DEGs) showed that four metabolic pathways responsible for combating Cd stress were commonly regulated in the three organisms, including antioxidant reactions, sulfur metabolism, cell wall remodeling, and metal transport. In vivo expression patterns of 43 DEGs from the four pathways were further examined using quantitative PCR and resulted in a relatively comparable dynamic of gene expression patterns with transcriptome sequencing (RNA-seq). Cross-kingdom comparison of typical Cd stress-responding proteins resulted in the detection of 12 groups of homologous proteins in the three species. A class of potential metal transporters were subjected to cross-transformation to test their functional complementation. An ABC transporter gene in E. coli, possibly homologous to the yeast ycf1, was heterologously expressed in S. cerevisiae, resulting in enhanced Cd tolerance. Overall, our findings indicated that conserved genetic modules against Cd toxicity were commonly regulated among distantly related microbial species, which will be helpful for utilizing them in modifying microbial traits for bioremediation.

IMPORTANCE Research is establishing a systems biology view of biological response to Cd stress. It is meaningful to explore whether there is regulatory isomorphy among distantly related organisms. A transcriptomic comparison was done among model microbes, leading to the identification of a conserved cellular model pinpointing the generic strategies utilized by microbes for combating Cd stress. A novel E. coli transporter gene substantially increased yeast’s Cd tolerance. Knowledge on systems understanding of the cellular response to metals provides the basis for developing bioengineering remediation technology.

Comparative Transcriptomic Analysis of Root Cadmium Responses in Two Chinese Rice Cultivars Yuzhenxiang and Xiangwanxian 12

Cadmium (Cd) pollution in paddy soil is an increasingly serious issue in rice production. It has been reported that there is a higher or lower grain Cd accumulation in the rice cultivars Yuzhenxiang (YZX) or Xiangwanxian 12 (XWX), respectively. To better manage the Cd pollution problem, the genes that might play vital roles in governing the difference in root Cd responses between these two rice cultivars were examined. In this study, the results of RNA sequencing (RNA-seq) showed that there were 341 and 161 differentially expressed genes in the roots of YZX and XWX after Cd exposure, respectively. Among these genes, 7 genes, such as Os06g0196300 (OsJ_019618), Os07g0570700 (OsJ_24808), ADI1, GDCSH, HSFB2C, PEX11-4, and CLPB1, possessed higher degree nodes with each other, through interaction analysis by the STRING (search tool for the retrieval of interacting genes/proteins) software, suggesting that they might play vital roles in Cd response. Based on GO enrichment analysis, 41 differently expressed genes after Cd treatment in YZX or XWX were identified to be related to Cd response. Through comparative transcriptomic analysis, 257 genes might be associated with the root Cd response difference between YZX and XWX. Furthermore, we supposed that ADI1, CFBP1, PEX11-4, OsJ_019618, OsJ_24808, GDCSH, CLPB1, LAC6, and WNK3 might be implicated in Cd response based on the combined analysis of RT-qPCR, interaction, and GO annotation analysis. In conclusion, the numerous genes that might be related to Cd stress response and root Cd response difference between YZX and XWX at the booting stage may be of benefit for the development of rice varieties with low Cd consumption.

Salicylic acid reduces cadmium (Cd) accumulation in rice (Oryza sativa L.) by regulating root cell wall composition via nitric oxide signaling

The effects of salicylic acid (SA) on cadmium (Cd) accumulation, Cd subcellular distribution, cell wall composition and Cd adsorption in Cd-stressed rice seedlings were examined. The interaction between SA and nitric oxide (NO) signaling in regulating cell wall composition under Cd exposure was also investigated. Our results showed that 5 μmol·L^-1 Cd treatment significantly decreased plant height, root length and plant dry weight by 40.1%, 46.1% and 21.3% (p < 0.05), respectively, and the inhibitory effects of Cd on the growth parameters were alleviated by exogenous SA. Application of SA remarkably decreased Cd concentrations in roots and shoots of rice seedlings by 48.0% and 19.6%, respectively, and increased the distribution ratio of Cd in the root cell wall fraction (from 35.7% to 40.6%) compared with Cd treatment alone. The reduced Cd accumulation in rice plants could be attributed to that SA application promoted pectin synthesis and demethylesterification, thereby increasing Cd deposition in the root cell wall. Moreover, SA application promoted lignin biosynthesis to strengthen the cell wall and prevent Cd from entering the root cells. In addition, NO might be involved in SA-induced pectin synthesis, pectin demethylesterification and lignin biosynthesis as a downstream signaling molecule, contributing to reduced Cd accumulation in Cd-stressed rice seedlings. The results provide deep insights into the mechanisms of exogenous SA action in reducing Cd accumulation in rice plants.

Phytoexclusion of heavy metals using low heavy metal accumulating cultivars: A green technology

Heavy metal (HM) pollution of farmland is a serious problem worldwide and consumption of HM-contaminated food products poses significant public health risks. Phytoexclusion using low HM accumulating cultivars (LACs) is a promising and practical technology to mitigate the risk of HM contamination of agricultural products grown in polluted soils, and does not alter cultivation practices, is easy to apply, and is economical. This review provides an overview of the major scientific advances accomplished in the field of LACs worldwide. The LACs concept and identification criteria are presented, and the known LACs among currently cultivated grain crops and vegetables are re-evaluated. The low HM accumulation by LACs is affected by crop ecophysiological features and soil physicochemical characteristics. Taking low Cd accumulating cultivars as an example, it is known that they can efficiently exclude Cd from entering their edible parts in three ways: 1) decrease in root Cd uptake by reducing organic acids secretion in the rhizosphere and transport protein production; 2) restriction of Cd translocation from roots to shoots via enhanced Cd retention in the cell wall and Cd sequestration in vacuoles; and 3) reduction in Cd translocation from shoots to grains by limiting Cd redirection and remobilization mediated through nodes. We propose an LAC application strategy focused on LACs and optimized to work with other agronomic measures according to the classification of HM risk level for LACs, providing a cost-effective and practical solution for safe utilization of large areas of farmland polluted with low to moderate levels of HMs.

Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress

N⁶-methyladenosine (m⁶A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m⁶A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m⁶A modification has become feasible. A study suggested that m⁶A modification is crucial for posttranscriptional regulation related to Cd²⁺-induced malignant transformation, but the association between m⁶A modification in plants and Cd tolerance has not been reported. We investigated the m⁶A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m⁶A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m⁶A peaks in cv. 9311 and 2,065 differential m⁶A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m⁶A peaks indicated that the "phenylalanine", "tyrosine and tryptophan biosynthesis", "glycine", "adherens junctions", "glycerophospholipid metabolism" and "threonine metabolism" signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The "arginine", "proline metabolism", "glycerolipid", and "protein processing in endoplasmic reticulum" metabolism pathways were significantly enriched in genes with differentially modified m⁶A peaks in cv. NIP. Unlike that in Arabidopsis, the m⁶A-modified nucleotide position on mRNAs (m⁶A peak) distribution in rice exhibited a preference towards both the stop codon and 3' untranslated regions (3' UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m⁶A modification in RNA in plants.

Breeding for low cadmium accumulation cereals

Cadmium (Cd) is an element that is nonessential and extremely toxic to both plants and human beings. Soil contaminated with Cd has adverse impacts on crop yields and threatens human health via the food chain. Cultivation of low-Cd cultivars has been of particular interest and is one of the most cost-effective and promising approaches to minimize human dietary intake of Cd. Low-Cd crop cultivars should meet particular criteria, including acceptable yield and quality, and their edible parts should have Cd concentrations below maximum permissible concentrations for safe consumption, even when grown in Cd-contaminated soil. Several low-Cd cereal cultivars and genotypes have been developed worldwide through cultivar screening and conventional breeding. Molecular markers are powerful in facilitating the selection of low-Cd cereal cultivars. Modern molecular breeding technologies may have great potential in breeding programs for the development of low-Cd cultivars, especially when coupled with conventional breeding. In this review, we provide a synthesis of low-Cd cereal breeding.

Water management affects arsenic uptake and translocation by regulating arsenic bioavailability, transporter expression and thiol metabolism in rice (Oryza sativa L.)

Water management is an economic and effective strategy to reduce arsenic (As) accumulation in rice grains, but little is known about the effect of water management on the migration and transformation of As in the soil-rice system. In this study, the effect of the continually (CF) and intermittent flooding (IF) treatments on the dynamic change of As in the rhizosphere soil-pore water-iron plaque-rice system was systematically investigated using pot experiments. The expressions of genes involved in As uptake and translocation in rice plants under different water management treatments were further examined. Results showed that the total As concentration in brown rice was increased by 50.8% in the CF treatment compared to the IF treatment, and dimethylarsinic acid (DMA) made greater contribution (from 15.5% to 29.2%) to total As increase in brown rice under the CF treatment. The CF treatment increased As bioavailability in the rhizosphere soil and soil pore water, which enhanced As uptake and transport to the xylem in rice plants by inducing the expressions of silicon transporter genes (OsLsi1 and OsLsi2) compared to the IF treatment. Moreover, the CF treatment increased As translocation from roots to shoots by reducing soil available sulfur and phytochelatins (PCs) biosynthesis and vacuolar sequestration in rice roots compared with the IF treatment. The study provides insight into the physiological and molecular mechanisms underlying As uptake and translocation in rice plants under different water regimes, which will be helpful for adopting the irrigation technique to mitigate excessive As accumulation in rice grains and associated health risk to humans.

Whole-transcriptome sequencing (RNA-seq) study of the ZFL zebrafish liver cell line after acute exposure to Cd2+ ions

Cadmium (Cd) is a non-essential metal with no known biological function and a broad range of toxic effects in biological systems. We used whole-transcriptome sequencing (RNA-seq) to study the effects of Cd²⁺ toxicity in zebrafish liver cells, ZFL. The results of an RNA-Seq analysis of ZFL cells exposed to 5, 10 or 20 μM Cd²⁺ for 4- or 24-h. The differentially expressed genes affected by Cd²⁺ were analyzed by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to study the regulated pathways. Cd²⁺ regulated the expression of genes associated with cellular Cu, Zn, and Fe homeostasis, DNA replication leading to cell cycle arrest and apoptosis, and glutathione metabolism. Cd²⁺ boosted up the amino acid synthesis, possibly to support the glutathione metabolism for tackling the oxidative stress generated from Cd²⁺. Cd²⁺ stimulation was similar to heat or xenobiotics, based on the responses from ZFL such as endoplasmic reticulum stress and protein folding. We linked also those finding of gene activations relating to carcinogenesis of Cd. This paper provides a comprehensive analysis of the expression profiles induced by Cd²⁺ exposure in ZFL cells, as well as useful insights into the specific toxic effects.

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.

Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns

Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

Hybrid rice cultivars are widely planted around the world. Here, the authors resequence 1,143 indica accessions, focusing on the parents of superior hybrid rice lines in China, and reveal genetic loci that are associated with heterosis via measuring frequency of parental variation difference (FPVD).

Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves

Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha-1), Se (500 g ha-1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.

Cadmium isotope fractionation reveals genetic variation in Cd uptake and translocation by Theobroma cacao and role of natural resistance-associated macrophage protein 5 and heavy metal ATPase-family transporters

In response to new European Union regulations, studies are underway to mitigate accumulation of toxic cadmium (Cd) in cacao (Theobroma cacao, Tc). This study advances such research with Cd isotope analyses of 19 genetically diverse cacao clones and yeast transformed to express cacao natural resistance-associated macrophage protein (NRAMP5) and heavy metal ATPases (HMAs). The plants were enriched in light Cd isotopes relative to the hydroponic solution with Δ114/110Cdtot-sol = -0.22 ± 0.08‰. Leaves show a systematic enrichment of isotopically heavy Cd relative to total plants, in accord with closed-system isotope fractionation of Δ114/110Cdseq-mob = -0.13‰, by sequestering isotopically light Cd in roots/stems and mobilisation of remaining Cd to leaves. The findings demonstrate that (i) transfer of Cd between roots and leaves is primarily unidirectional; (ii) different clones utilise similar pathways for Cd sequestration, which differ from those of other studied plants; (iii) clones differ in their efficiency of Cd sequestration. Transgenic yeast that expresses TcNRAMP5 (T. cacao natural resistance-associated macrophage gene) had isotopically lighter Cd than did cacao. This suggests that NRAMP5 transporters constitute an important pathway for uptake of Cd by cacao. Cd isotope signatures of transgenic yeast expressing HMA-family proteins suggest that they may contribute to Cd sequestration. The data are the first to record isotope fractionation induced by transporter proteins in vivo.