Multi-omics analysis reveals differential molecular responses to cadmium toxicity in rice root tip and mature zone

Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants

Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro-ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd-containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops.

Root-zone regulation and longitudinal translocation cause intervarietal differences for phthalates accumulation in vegetables

Selecting and cultivating low-accumulating crop varieties (LACVs) is the most effective strategy for the safe utilization of di-(2-ethylhexyl) phthalate (DEHP)-contaminated soils, promoting cleaner agricultural production. However, the adsorption-absorption-translocation mechanisms of DEHP along the root-shoot axis remains a formidable challenge to be solved, especially for the research and application of LACV, which are rarely reported. Here, systematic analyses of the root surface ad/desorption, root apexes longitudinal allocation, uptake and translocation pathway of DEHP in LACV were investigated compared with those in a high-accumulating crop variety (HACV) in terms of the root-shoot axis. Results indicated that DEHP adsorption was enhanced in HACV by root properties, elemental composition and functional groups, but the desorption of DEHP was greater in LACV than HACV. The migration of DEHP across the root surface was controlled by the longitudinal partitioning process mediated by root tips, where more DEHP accumulated in the root cap and meristem of LACV due to greater cell proliferation. Furthermore, the longitudinal translocation of DEHP in LACV was reduced, as evidenced by an increased proportion of DEHP in the root apoplast. The symplastic uptake and xylem translocation of DEHP were suppressed more effectively in LACV than HACV, because DEHP translocation in LACV required more energy, binding sites and transpiration. These results revealed the multifaceted regulation of DEHP accumulation in different choysum (Brassica parachinensis L.) varieties and quantified the pivotal regulatory processes integral to LACV formation.

The colonization of Penicillium oxalicum SL2 on rice root surface increased Pb interception capacity of iron plaque and decreased Pb uptake by roots

The exploration of microbial resources to reduce Pb accumulation in rice attracted great attention. In this study, we found Penicillium oxalicum SL2, a Pb-tolerant strain with good capability of dissolving phosphorus and stabilizing Pb in soil, was able to colonize on the root surface of rice seedlings without additional carbon sources, and promoted the secretion of metabolites related to amino acid metabolism, organic acid metabolism, signal transduction and other pathways in rhizosphere exudates, in which the secretion of oxalate increased by 47.7 %. However, P. oxalicum SL2 increased Fe(II) proportion and Fe availability on the root surface, resulting in iron plaque content decrease. Moreover, by converting root surface Pb from Pb-Fe state to PbC2O4 and Pb-P compounds, P. oxalicum SL2 increased Pb intercept capacity of iron plaque by 118.0 %. Furthermore, P. oxalicum SL2 regulated element distribution on the root surface, and reduced the relative content of Pb on the maturation zone of root tip, which was conducive to reducing Pb uptake by apoplastic pathway and the risk of Pb accumulation in root system. Our findings further revealed the interaction between P. oxalicum SL2 and rice root, providing a theoretical basis for the development and application of microbial agents in Pb-contaminated farmland.

Progress in Rice Breeding Based on Genomic Research

The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.

Multi-Omics Analysis Reveals the Distinct Features of Metabolism Pathways Supporting the Fruit Size and Color Variation of Giant Pumpkin

Pumpkin (Cucurbita maxima) is an important vegetable crop of the Cucurbitaceae plant family. The fruits of pumpkin are often used as directly edible food or raw material for a number of processed foods. In nature, mature pumpkin fruits differ in size, shape, and color. The Atlantic Giant (AG) cultivar has the world's largest fruits and is described as the giant pumpkin. AG is well-known for its large and bright-colored fruits with high ornamental and economic value. At present, there are insufficient studies that have focused on the formation factors of the AG cultivar. To address these knowledge gaps, we performed comparative transcriptome, proteome, and metabolome analysis of fruits from the AG cultivar and a pumpkin with relatively small fruit (Hubbard). The results indicate that up-regulation of gene-encoded expansins contributed to fruit cell expansion, and the increased presence of photoassimilates (stachyose and D-glucose) and jasmonic acid (JA) accumulation worked together in terms of the formation of large fruit in the AG cultivar. Notably, perhaps due to the rapid transport of photoassimilates, abundant stachyose that was not converted into glucose in time was detected in giant pumpkin fruits, implying that a unique mode of assimilate unloading is in existence in the AG cultivar. The potential molecular regulatory network of photoassimilate metabolism closely related to pumpkin fruit expansion was also investigated, finding that three MYB transcription factors, namely CmaCh02G015900, CmaCh01G018100, and CmaCh06G011110, may be involved in metabolic regulation. In addition, neoxanthin (a type of carotenoid) exhibited decreased accumulation that was attributed to the down-regulation of carotenoid biosynthesis genes in AG fruits, which may lead to pigmentation differences between the two pumpkin cultivars. Our current work will provide new insights into the potential formation factors of giant pumpkins for further systematic elucidation.

Transcriptome-wide m6A methylation profiling identifies GmAMT1;1 as a promoter of lead and cadmium tolerance in soybean nodules

Lead (Pb) and cadmium (Cd) are common heavy metal pollutants that are often found in the soil in soybean agricultural production, adversely impacting symbiotic nitrogen fixation in soybean nodules. In this study, the exposure of soybean nodules to Pb and Cd stress was found to reduce nitrogenase activity. Shifts in the RNA methylation profiles of nodules were subsequently examined by profiling the differential expression of genes responsible for regulating m6A modifications and conducting transcriptome-wide analyses of m6A methylation profiles under Pb and Cd stress condition. Differentially methylated genes (DMGs) that were differentially expressed were closely related to reactive oxygen species activity and integral membrane components. Overall, 19 differentially expressed DMGs were ultimately determined to be responsive to both Pb and Cd stress, including Glyma.20G082450, which encodes GmAMT1;1 and was confirmed to be a positive regulator of nodules tolerance to Pb and Cd. Together, these results are the first published data corresponding to transcriptome-wide m6A methylation patterns in soybean nodules exposed to Cd and Pb stress, and provide novel molecular insight into the regulation of Pb and Cd stress responses in nodules, highlighting promising candidate genes related to heavy metal tolerance, that may also be amenable to application in agricultural production. ENVIRONMENTAL IMPLICATIONS: Lead (Pb) and cadmium (Cd) are prevalent heavy metal pollutants in soil, and pose a major threat to crop production, food security and human health. Here, MeRIP-seq approach was employed to analyze the regulatory network activated in soybean nodules under Pb and Cd stress, ultimately leading to the identification of 19 shared differentially expressed DMGs. When overexpressed, GmATM1;1 was found to enhance the Pb and Cd tolerance of soybean nodules. These results provide a theoretical basis for studies on tolerance to heavy metals in symbiotic nitrogen fixation, and provide an approach to enhancing Pb and Cd tolerance in soybean production.

Multi-omics analysis reveals the biosynthesis of flavonoids during the browning process of Malus sieversii explants

Malus sieversii is a precious apple germplasm resource. Browning of explants is one of the most important factors limiting the survival rate of plant tissue culture. In order to explore the molecular mechanism of the browning degree of different strains of Malus sieversii, we compared the dynamic changes of Malus sieversii and Malus robusta Rehd. during the whole browning process using a multi-group method. A total of 44 048 differentially expressed genes (DEGs) were identified by transcriptome analysis on the DNBSEQ-T7 sequencing platform. KEGG enrichment analysis showed that the DEGs were significantly enriched in the flavonoid biosynthesis pathway. In addition, metabonomic analysis showed that (-)-epicatechin, astragalin, chrysin, irigenin, isoquercitrin, naringenin, neobavaisoflavone and prunin exhibited different degrees of free radical scavenging ability in the tissue culture browning process, and their accumulation in different varieties led to differences in the browning degree among varieties. Comprehensive transcriptome and metabonomics analysis of the data related to flavonoid biosynthesis showed that PAL, 4CL, F3H, CYP73A, CHS, CHI, ANS, DFR and PGT1 were the key genes for flavonoid accumulation during browning. In addition, WGCNA analysis revealed a strong correlation between the known flavonoid structure genes and the selected transcriptional genes. Protein interaction predictions demonstrated that 19 transcription factors (7 MYBs and 12 bHLHs) and 8 flavonoid structural genes had targeted relationships. The results show that the interspecific differential expression of flavonoid genes is the key influencing factor of the difference in browning degree between Malus sieversii and Malus robusta Rehd., providing a theoretical basis for further study on the regulation of flavonoid biosynthesis.

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.