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This review archives the achievements made in the last two decades and presents a brief outline of some significant factors influencing the Agrobacterium-mediated transformation of Sorghum bicolor. Recently, progress in successful transformation has been made for this particular monocot crop through direct DNA delivery method and indirect method via Agrobacterium. However, lower transformation rate still proved to be a bottleneck in genetic modification of sorghum. An efficient Agrobacterium transformation system could be attained by optimizing the preliminary assays, comprising of explant source, growth media, antibiotics, Agrobacterium strains and agro-infection response of callus. The selection of competent strains for genetic transformation is also one of the key factors of consideration. Successful transformation is highly dependent on genome configuration of selected cultivar, where non-tannin genotype proved the best suited. Immature embryos from the field source have higher inherent adaptation chances than that of the greenhouse source. A higher concentration of Agrobacterium may damage the explant source. Utilization of anti-necrotic treatments and optimized tissue culture timeframe are the adequate strategies to lower down the effect of phenolic compounds. Appropriate selection of culture media vessels at different stages of tissue culture may also assist in a constructive manner. In conclusion, some aspects such as culture environment with medium composition, explant sources, and genotypes play an indispensable role in successful Agrobacterium-mediated sorghum transformation system.

In addition to phytate, polyphenols (PP) might contribute to low Fe bioavailability from sorghum-based foods. To investigate the inhibitory effects of sorghum PP on Fe absorption and the potential enhancing effects of ascorbic acid (AA), NaFeEDTA and the PP oxidase enzyme laccase, we carried out three Fe absorption studies in fifty young women consuming dephytinised Fe-fortified test meals based on white and brown sorghum varieties with different PP concentrations. Fe absorption was measured as the incorporation of stable Fe isotopes into erythrocytes. In study 1, Fe absorption from meals with 17 mg PP (8·5 %) was higher than that from meals with 73 mg PP (3·2 %) and 167 mg PP (2·7 %; P< 0·001). Fe absorption from meals containing 73 and 167 mg PP did not differ (P= 0·9). In study 2, Fe absorption from NaFeEDTA-fortified meals (167 mg PP) was higher than that from the same meals fortified with FeSO4 (4·6 v. 2·7 %; P< 0·001), but still it was lower than that from FeSO4-fortified meals with 17 mg PP (10·7 %; P< 0·001). In study 3, laccase treatment decreased the levels of PP from 167 to 42 mg, but it did not improve absorption compared with that from meals with 167 mg PP (4·8 v. 4·6 %; P= 0·4), whereas adding AA increased absorption to 13·6 % (P< 0·001). These findings suggest that PP from brown sorghum contribute to low Fe bioavailability from sorghum foods and that AA and, to a lesser extent, NaFeEDTA, but not laccase, have the potential to overcome the inhibitory effect of PP and improve Fe absorption from sorghum foods.

Low availability of nitrogen (N) is often a major limiting factor to crop yield in most nutrient-poor soils. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most land plants that enhance plant nutrient uptake, particularly of phosphate. A growing number of reports point to the substantially increased N accumulation in many mycorrhizal plants; however, the contribution of AM symbiosis to plant N nutrition and the mechanisms underlying the AM-mediated N acquisition are still in the early stages of being understood. Here, we report that inoculation with AM fungus Rhizophagus irregularis remarkably promoted rice (Oryza sativa) growth and N acquisition, and about 42% of the overall N acquired by rice roots could be delivered via the symbiotic route under N-NO₃⁻ supply condition. Mycorrhizal colonization strongly induced expression of the putative nitrate transporter gene OsNPF4.5 in rice roots, and its orthologs ZmNPF4.5 in Zea mays and SbNPF4.5 in Sorghum bicolor. OsNPF4.5 is exclusively expressed in the cells containing arbuscules and displayed a low-affinity NO₃⁻ transport activity when expressed in Xenopus laevis oocytes. Moreover, knockout of OsNPF4.5 resulted in a 45% decrease in symbiotic N uptake and a significant reduction in arbuscule incidence when NO₃⁻ was supplied as an N source. Based on our results, we propose that the NPF4.5 plays a key role in mycorrhizal NO₃⁻ acquisition, a symbiotic N uptake route that might be highly conserved in gramineous species.

Background The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood. Results Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype. Conclusions The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop.

Sorghum is emerging as an excellent genetic model for the design of C₄ grass bioenergy crops. Annual energy Sorghum hybrids also serve as a source of biomass for bioenergy production. Elucidation of Sorghum’s flowering time gene regulatory network, and identification of complementary alleles for photoperiod sensitivity, enabled large-scale generation of energy Sorghum hybrids for testing and commercial use. Energy Sorghum hybrids with long vegetative growth phases were found to accumulate more than twice as much biomass as grain Sorghum, owing to extended growing seasons, greater light interception, and higher radiation use efficiency. High biomass yield, efficient nitrogen recycling, and preferential accumulation of stem biomass with low nitrogen content contributed to energy Sorghum’s elevated nitrogen use efficiency. Sorghum’s integrated genetics-genomics-breeding platform, diverse germplasm, and the opportunity for annual testing of new genetic designs in controlled environments and in multiple field locations is aiding fundamental discovery, and accelerating the improvement of biomass yield and optimization of composition for biofuels production. Recent advances in wide hybridization between Sorghum and other C₄ grasses could allow the deployment of improved genetic designs of annual energy Sorghums in the form of wide-hybrid perennial crops. The current trajectory of energy Sorghum genetic improvement indicates that it will be possible to sustainably produce biofuels from C₄ grass bioenergy crops that are cost competitive with petroleum-based transportation fuels.

Micronutrient deficiencies are common in locales where people must rely upon sorghum as their staple diet. Sorghum grain is seriously deficient in provitamin A (β-carotene) and in the bioavailability of iron and zinc. Biofortification is a process to improve crops for one or more micronutrient deficiencies. We have developed sorghum with increased β-carotene accumulation that will alleviate vitamin A deficiency among people who rely on sorghum as their dietary staple. However, subsequent β-carotene instability during storage negatively affects the full utilization of this essential micronutrient. We determined that oxidation is the main factor causing β-carotene degradation under ambient conditions. We further demonstrated that coexpression of homogentisate geranylgeranyl transferase (HGGT), stacked with carotenoid biosynthesis genes, can mitigate β-carotene oxidative degradation, resulting in increased β-carotene accumulation and stability. A kinetic study of β-carotene degradation showed that the half-life of β-carotene is extended from less than 4 wk to 10 wk on average with HGGT coexpression.

Drought stress triggers mature leaf senescence, which supports plant survival and remobilization of nutrients; yet leaf senescence also critically decreases post-drought crop yield. Drought generally results in carbon/nitrogen imbalance, which is reflected in the increased carbon:nitrogen (C:N) ratio in mature leaves, and which has been shown to be involved in inducing leaf senescence under normal growth conditions. Yet the involvement of the carbon/nitrogen balance in regulation of drought-induced leaf senescence is unclear. To investigate the role of carbon/nitrogen balance in drought-induced senescence, sorghum seedlings were subjected to a gradual soil drought treatment. Leaf senescence symptoms and the C:N ratio, which was indicated by the ratio of non-structural carbohydrate to total N content, were monitored during drought progression. In this study, leaf senescence developed about 12 days after the start of drought treatment, as indicated by various senescence symptoms including decreasing photosynthesis, photosystem II photochemistry efficiency (Fv/Fm) and chlorophyll content, and by the differential expression of senescence marker genes. The C:N ratio was significantly enhanced 10 to 12 days into drought treatment. Leaf senescence occurred in the older (lower) leaves, which had higher C:N ratios, but not in the younger (upper) leaves, which had lower C:N ratios. In addition, a detached leaf assay was conducted to investigate the effect of carbon/nitrogen availability on drought-induced senescence. Exogenous application of excess sugar combined with limited nitrogen promoted drought-induced leaf senescence. Thus our results suggest that the carbon/nitrogen balance may be involved in the regulation of drought-induced leaf senescence.

Summary Cadmium (Cd) is a widespread soil contaminant threatening human health. As an ideal energy plant, sweet sorghum (Sorghum bicolor (L.) Moench) has great potential in phytoremediation of Cd‐polluted soils, although the molecular mechanisms are largely unknown. In this study, key factors responsible for differential Cd accumulation between two contrasting sweet sorghum genotypes (high‐Cd accumulation one H18, and low‐Cd accumulation one L69) were investigated. H18 exhibited a much higher ability of Cd uptake and translocation than L69. Furthermore, Cd uptake through symplasmic pathway and Cd concentrations in xylem sap were both higher in H18 than those in L69. Root anatomy observation found the endodermal apoplasmic barriers were much stronger in L69, which may restrict the Cd loading into xylem. The molecular mechanisms underlying these morpho‐physiological traits were further dissected by comparative transcriptome analysis. Many genes involved in cell wall modification and heavy metal transport were found to be Cd‐responsive DEGs and/or DEGs between these two genotypes. KEGG pathway analysis found phenylpropanoid biosynthesis pathway was over‐represented, indicating this pathway may play important roles in differential Cd accumulation between two genotypes. Based on these results, a schematic representation of main processes involved in differential Cd uptake and translocation in H18 and L69 is proposed, which suggests that higher Cd accumulation in H18 depends on a multilevel coordination of efficient Cd uptake and transport, including efficient root uptake and xylem loading, less root cell wall binding, and weaker endodermal apoplasmic barriers.

The WRKY transcription factor family is involved in responding to biotic and abiotic stresses. Its members contain a typical WRKY domain and can regulate plant physiological responses by binding to W-boxes in the promoter regions of downstream target genes. We identified the sweet sorghum SbWRKY50 (Sb09g005700) gene, which encodes a typical class II of the WRKY family protein that localizes to the nucleus and has transcriptional activation activity. The expression of SbWRKY50 in sweet sorghum was reduced by salt stress, and its ectopic expression reduced the salt tolerance of Arabidopsis thaliana plants. Compared with the wild type, the germination rate, root length, biomass and potassium ion content of SbWRKY50 over-expression plants decreased significantly under salt-stress conditions, while the hydrogen peroxide, superoxide anion and sodium ion contents increased. Real-time PCR results showed that the expression levels of AtSOS1, AtHKT1 and genes related to osmotic and oxidative stresses in over-expression strains decreased under salt-stress conditions. Luciferase complementation imaging and yeast one-hybrid assays confirmed that SbWRKY50 could directly bind to the upstream promoter of the SOS1 gene in A. thaliana. However, in sweet sorghum, SbWRKY50 could directly bind to the upstream promoters of SOS1 and HKT1. These results suggest that the new WRKY transcription factor SbWRKY50 participates in plant salt response by controlling ion homeostasis. However, the regulatory mechanisms are different in sweet sorghum and Arabidopsis, which may explain their different salt tolerance levels. The data provide information that can be applied to genetically modifying salt tolerance in different crop varieties.Key message(1) Sweet sorghum SbWRKY50 is negatively involved in salt response.(2) Over-expression of SbWRKY50 in A. thaliana affects plant growth, ROS and the ion contents.(3) SbWRKY50 could directly bind to the upstream promoter of the SOS1 gene in A. thaliana and the promoter of SOS1 and HKT1 in sweet sorghum.

Elucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predicting gene expression profiles from gene flanking regions of the plant species Arabidopsis thaliana , Solanum lycopersicum , Sorghum bicolor , and Zea mays . With over 80% accuracy, our models enabled predictive feature selection, highlighting e.g . the significant role of UTR regions in determining gene expression levels. The models demonstrated remarkable cross-species performance, effectively identifying both conserved and species-specific regulatory sequence features and their predictive power for gene expression. We illustrated the application of our approach by revealing causal links between genetic variation and gene expression changes across fourteen tomato genomes. Lastly, our models efficiently predicted genotype-specific expression of key functional gene groups, exemplified by underscoring known phenotypic and metabolic differences between Solanum lycopersicum and its wild, drought-resistant relative, Solanum pennellii . This study explores the variation in gene regulation across plant species and genotypes using interpretable deep learning on DNA sequence and RNA-seq data, demonstrating the models’ utility in functional genomics and phenotypic trait prediction.